UCLA Miniscope - User contributions [en]

Online Workshop

2019-10-17T14:58:48Z

Tristanshuman: /* Surgery Procedure and Baseplating */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).

== MCCS Miniscope Workshop 2018 ==

'''The link below takes you to the slides and talks presented at our previous MCCS Miniscope Workshop. This is likely the best place to start when learning about the UCLA Miniscope project.'''

[https://vimeopro.com/user16212450/mini-scope-workshop-11-01-2018/video/300830371 MCCS Miniscope Workshop 2018 Recording]

== Imaging Principles and Microscope Design ==
[https://drive.google.com/open?id=0B1RSzZP5s3hhQ2RKQXpBcThVUVk Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/open?id=1SluR4GEHCjsx5AgHavIukomudr8-3f6W Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://ucla.box.com/s/qd4aikyy1tk3iciqgfx73urr6dcc45mv Sample Imaging Data]

[https://drive.google.com/open?id=0B1RSzZP5s3hhcFVhRm9QVW5fUHM Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[[Initial Testing of Assembled Miniscopes]]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Surgery Protocol

2019-10-17T14:55:32Z

Tristanshuman: /* Relay Baseplating */

The following is a basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging. For videos of surgery and baseplating, see the [[Online Workshop]]. Also, see the recent Nature Protocols paper from the Stuber Lab ([http://www.nature.com/nprot/journal/v11/n3/full/nprot.2016.021.html link]) that has a very detailed description of the surgery.

In order to image, animals will need to undergo three surgical procedures: a virus injection, a GRIN lens implantation, and baseplate attachment.

== Virus Injection ==
Before implanting the GRIN lens, you will need to inject a fluorescent indicator such as GCaMP6. We have generally used AAV1.Syn.GCaMP6f.WPRE.SV40 from Penn Vector (Item number AV-1-PV2822) and had great success in dorsal CA1. You may also be able to use GCaMP6 transgenic mice, but we have not tested whether any of the newer lines are bright enough to be imaged.

== GRIN Lens Implantation==

=== Basic Equipment Needed ===
You will only need basic surgical equipment to perform GRIN lens implantation surgeries. This includes a mouse stereotax, an isoflurane vaporizor, surgical heat pad, stereo surgical microscope, light source, dental drill, and bead sterilizer. For recommended equipment, see the master [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].

You will need the following basic tools and supplies: fine forceps, blunt forceps, fine scissors, scalpel and blade, small skull screws, drill bits, cyanoacrylate glue, dental cement, Kwik-Sil, and [[cortex buffer]]

=== Aspirator and Lens Holder ===
You will need an aspirator to remove cortex above the hippocampus. This can be built very simply with a vacuum line (or pump), a liquid trap, 1 ml syringe (with a hole to control suction), blunt needles, tubing and connectors, and hot glue.
[[File:Aspirator.PNG|center|500px]]

You can easily build a GRIN lens holder by using a suction system to hold the lens in place as it is dropped into the brain for implantation. To build, start with two 1ml micropipette tips. Cut the first so that the tip is just larger than the diameter of the GRIN lens you will be using. Cut the second tip so that the end is just smaller than the size of the GRIN lens. Connect this end to a 1ml syringe and connect to a vacuum line. This will then hold the lens in place during implantation. You can then use tape to attach this holder to a stereotax. Another solution we have used is a basic drill chuck, but this is only good for large (2mm) lenses.
[[File:LensHolder.PNG|center|500px]]

=== Skull Preparation ===
You must first prepare the skull for implantation. We recommend shaving the head area and sterilizing with 3 alternating betadine and ethanol scrubs. Next, remove the scalp with scissors and clean the skull with hydrogen peroxide and saline. Scrape and score the skull to increase the bond with the glue. We also detach the neck muscle from the skull in order to reduce pull on the skull and prevent muscle growth that can make the implant less stable. Finally we insert a skull screw on the opposite side of the skull to enhance the stability of the implant.

=== Craniotomy and Aspiration ===
Using a stereotax, align the skull and find the location for the implant. Using a drill, make 4 guide holes to outline the lens placement. For CA1, we recommend offsetting the lens 0.5mm to the medial side of the virus injection to prevent imaging any damage induced by the virus injection. Connect the guide holes to create a circular craniotomy and peel off the circular skull fragment. Do not worry about blood as the top layers of cortex will be removed by aspiration. Make absolutely sure that the craniotomy is at least the size of your GRIN lens! Cover with cortex buffer and scrape around the outside of the craniotomy to remove any excess bone or dura.

While keeping a constant flow of cortex buffer use the aspirator to slowly remove the cortex above the hippocampus. Continue removing cortex until you reach the white striations of the corpus callosum. Very slowly and carefully remove the horizontal white striations of the corpus callosum until you reach the striations that go vertical. When you reach these striations, stop aspirating and clean up the sides so that the lens can be placed into the brain. Continue washing with cortex buffer until all bleeding stops and keep the brain constantly flushed with cortex buffer.

=== Lens implantation ===
Attach GRIN lens to lens holder on stereotax. Align the lens with the top of the skull at the most posterior part of the craniotomy and quickly insert the lens 1.35 mm below the top of the skull. Remove any excess liquid with the aspirator. Connect the outside of the GRIN lens with the skull and skull screw using cyanoacrylate glue and let fully dry or use a glue accelerator. Remove the lens holder by simply removing the vacuum suction (you can just pinch the tubing) and withdrawing the holder. Next, cover the entire skull with cyanoacrylate glue, and then cover with dental cement. Let dry completely and cover with Kwik-Sil to protect the lens. Remove from stereotax and allow the animal to recover. Give the animal amoxicillin (or equivalent) for 7 days, and daily injections of carprofen and dexamethasone for 7 days.

=== Important tips to remember ===
*Try to keep the surgery as sterile as possible. Infections will destroy imaging and the ability to keep the same cells over many days.

*Try to keep isoflurane as low as possible. Surgeries can take 2-6 hours depending on experience.

*Aspirations will take a lot of practice. Go slow at first.

*Depth will be trial and error. If the first few animals don't give good images, check the depth using histology and adjust accordingly.

Please feel free to add any tips that you have!

== Baseplating Protocol ==

=== Basic Equipment needed ===
[[File:bp1.png|right|200px|thumb|Put a stack of magnets on a reference Miniscope and mark the top magnet to keep track of its polarity]]
[[File:bp2.png|right|200px|thumb|Magnetically attach the top magnet to screwdriver, coat with cyanoacrylate glue on the edge, and push through hole on baseplate]]
[[File:bp3.png|right|200px|thumb|Repeat for remaining two magnets; ensure top of baseplate is completely flat]]
[[File:bp4.png|right|200px|thumb|Coat bottom of baseplate with cyanoacrylate glue]]
[[File:bp5.png|right|200px|thumb|Score bottom and edges of baseplate with a dental drill]]
You will only need basic surgical equipment to baseplate. This includes a mouse stereotax, an isoflurane vaporizer, surgical heat pad, stereo surgical microscope, light source, and a dental drill.

You will also need cyanoacrylate glue, fine forceps, double distilled water, lens paper, and dental cement

=== Baseplate Preparation ===
Before affixing the baseplate on an animal, you will need to prepare the baseplate.
The first step is to insert magnets into the appropriate holes on the baseplate. To ensure that the polarity of the magnets is correct throughout the baseplate preparation, use a reference Miniscope to hold onto the magnets. Mark the top magnet with a sharpie, as seen in the picture to the right. Next, put the top magnet on the head of a screwdriver with the marked side facing away from the screwdriver. Apply cyanoacrylate glue on the edge of the magnet, then push the magnet through the appropriate hole. Ensure that the magnet goes through the hole completely and the top side of the baseplate is flat, as the quality of imaging relies on the Miniscope sitting flush on the baseplate. Repeat this procedure for the next 2 magnets. Finally, put a coat of cyanoacrylate glue on the bottom side of the baseplate and leave the baseplate to dry.
Once the baseplate has dried, score the bottom and the sides of the baseplate using a dental drill to allow the dental glue to adhere the baseplate and skull well.

{{#ev:youtube|https://youtu.be/z_32O2XoYI4|640|center}}

=== Cap Preparation ===
Similar to the baseplate preparation, use a reference Miniscope to hold onto the magnets. Mark the top magnet with a sharpie, and put the magnet on the head of a screwdriver with the marked side facing toward the screwdriver. Coat the magnet with cyanoacrylate glue and push the magnet into the appropriate hole. Repeat for the remaining two magnets.
=== Baseplating ===
Connect a Miniscope to a DAQ and initialize the Miniscope software on a computer. Attach your prepared baseplate onto the bottom of the Miniscope using a set screw.

Using a stereotax and isoflurane vaporizer, anesthetize the animal and fix ear bars until the animal is stable. Carefully remove the Kwik-Sil off the top of the animal’s GRIN lens with blunt forceps being sure not to scratch the lens. Under a stereo surgical microscope, check to see if there is debris on the top of the GRIN lens. If there is, dampen a sheet of lens paper using double distilled water. Wipe the top of the GRIN lens using fine forceps and lens paper, being sure to only wipe laterally and not to apply direct downward pressure.

After the top of the GRIN lens is clean, explore the field of view with the Miniscope. Adjust the LED brightness and focus accordingly. We advise that you use maximum gain and low LED excitation as to not photobleach the brain during baseplating. After finding your ideal view, practice taking the Miniscope off and on and finding the same view.

When you feel comfortable repeatedly finding the view with the Miniscope, apply dental cement in a “C” pattern around the GRIN lens, making sure not to touch the lens itself. It will be easier if your first application of dental cement is more viscous. Put the Miniscope on top of the lens and find your ideal view. Hold the Miniscope steadily as the first application of dental cement dries, making sure that your view does not change.
After the first application of dental cement dries, mix more dental cement and apply it on the posterior edge of the baseplate, making sure it seals to the skull. At this point, you can also build up dental cement along the wall of the baseplate on the animal’s right side. Be sure to avoid applying dental cement onto the camera itself and adhering it to the baseplate. Once the dental cement dries and you feel confident that the baseplate will no longer shift, carefully remove the Miniscope from the baseplate by unscrewing the set screw and lifting it off.

Apply dental cement to the anterior edge of the baseplate and fill in the gaps between the baseplate and skull on the animal’s left side. Allow the dental cement to dry and attach the plastic cap onto the top of the baseplate with a set screw.

{{#ev:youtube|https://youtu.be/GoDJGfqO3po|640|center}}

=== Relay Baseplating ===
If using a relay lens for deep imaging, you have 2 options for baseplating. First, you can secure the large objective GRIN lens into the Miniscope (see [[Imaging With Thin GRIN Lenses]]) and baseplate as you would with a single lens (see video above). If you use this method, you must make the objective lens very secure (with optical or Krazy glue) as any movement of that lens will change the focal plane of the image. Alternatively, you can cement that objective lens onto the animals head in order to make it more stable across imaging sessions. We have found this to be far better for stable recording of the same cells across weeks. The video below steps through this option and demonstrates how to secure the objective GRIN lens into place while imaging.

{{#ev:youtube|https://youtu.be/b-LrnOBX3j8|640|center}}

Surgery Protocol

2019-10-17T14:53:02Z

Tristanshuman: /* Relay Baseplating */

The following is a basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging. For videos of surgery and baseplating, see the [[Online Workshop]]. Also, see the recent Nature Protocols paper from the Stuber Lab ([http://www.nature.com/nprot/journal/v11/n3/full/nprot.2016.021.html link]) that has a very detailed description of the surgery.

In order to image, animals will need to undergo three surgical procedures: a virus injection, a GRIN lens implantation, and baseplate attachment.

== Virus Injection ==
Before implanting the GRIN lens, you will need to inject a fluorescent indicator such as GCaMP6. We have generally used AAV1.Syn.GCaMP6f.WPRE.SV40 from Penn Vector (Item number AV-1-PV2822) and had great success in dorsal CA1. You may also be able to use GCaMP6 transgenic mice, but we have not tested whether any of the newer lines are bright enough to be imaged.

== GRIN Lens Implantation==

=== Basic Equipment Needed ===
You will only need basic surgical equipment to perform GRIN lens implantation surgeries. This includes a mouse stereotax, an isoflurane vaporizor, surgical heat pad, stereo surgical microscope, light source, dental drill, and bead sterilizer. For recommended equipment, see the master [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].

You will need the following basic tools and supplies: fine forceps, blunt forceps, fine scissors, scalpel and blade, small skull screws, drill bits, cyanoacrylate glue, dental cement, Kwik-Sil, and [[cortex buffer]]

=== Aspirator and Lens Holder ===
You will need an aspirator to remove cortex above the hippocampus. This can be built very simply with a vacuum line (or pump), a liquid trap, 1 ml syringe (with a hole to control suction), blunt needles, tubing and connectors, and hot glue.
[[File:Aspirator.PNG|center|500px]]

You can easily build a GRIN lens holder by using a suction system to hold the lens in place as it is dropped into the brain for implantation. To build, start with two 1ml micropipette tips. Cut the first so that the tip is just larger than the diameter of the GRIN lens you will be using. Cut the second tip so that the end is just smaller than the size of the GRIN lens. Connect this end to a 1ml syringe and connect to a vacuum line. This will then hold the lens in place during implantation. You can then use tape to attach this holder to a stereotax. Another solution we have used is a basic drill chuck, but this is only good for large (2mm) lenses.
[[File:LensHolder.PNG|center|500px]]

=== Skull Preparation ===
You must first prepare the skull for implantation. We recommend shaving the head area and sterilizing with 3 alternating betadine and ethanol scrubs. Next, remove the scalp with scissors and clean the skull with hydrogen peroxide and saline. Scrape and score the skull to increase the bond with the glue. We also detach the neck muscle from the skull in order to reduce pull on the skull and prevent muscle growth that can make the implant less stable. Finally we insert a skull screw on the opposite side of the skull to enhance the stability of the implant.

=== Craniotomy and Aspiration ===
Using a stereotax, align the skull and find the location for the implant. Using a drill, make 4 guide holes to outline the lens placement. For CA1, we recommend offsetting the lens 0.5mm to the medial side of the virus injection to prevent imaging any damage induced by the virus injection. Connect the guide holes to create a circular craniotomy and peel off the circular skull fragment. Do not worry about blood as the top layers of cortex will be removed by aspiration. Make absolutely sure that the craniotomy is at least the size of your GRIN lens! Cover with cortex buffer and scrape around the outside of the craniotomy to remove any excess bone or dura.

While keeping a constant flow of cortex buffer use the aspirator to slowly remove the cortex above the hippocampus. Continue removing cortex until you reach the white striations of the corpus callosum. Very slowly and carefully remove the horizontal white striations of the corpus callosum until you reach the striations that go vertical. When you reach these striations, stop aspirating and clean up the sides so that the lens can be placed into the brain. Continue washing with cortex buffer until all bleeding stops and keep the brain constantly flushed with cortex buffer.

=== Lens implantation ===
Attach GRIN lens to lens holder on stereotax. Align the lens with the top of the skull at the most posterior part of the craniotomy and quickly insert the lens 1.35 mm below the top of the skull. Remove any excess liquid with the aspirator. Connect the outside of the GRIN lens with the skull and skull screw using cyanoacrylate glue and let fully dry or use a glue accelerator. Remove the lens holder by simply removing the vacuum suction (you can just pinch the tubing) and withdrawing the holder. Next, cover the entire skull with cyanoacrylate glue, and then cover with dental cement. Let dry completely and cover with Kwik-Sil to protect the lens. Remove from stereotax and allow the animal to recover. Give the animal amoxicillin (or equivalent) for 7 days, and daily injections of carprofen and dexamethasone for 7 days.

=== Important tips to remember ===
*Try to keep the surgery as sterile as possible. Infections will destroy imaging and the ability to keep the same cells over many days.

*Try to keep isoflurane as low as possible. Surgeries can take 2-6 hours depending on experience.

*Aspirations will take a lot of practice. Go slow at first.

*Depth will be trial and error. If the first few animals don't give good images, check the depth using histology and adjust accordingly.

Please feel free to add any tips that you have!

== Baseplating Protocol ==

=== Basic Equipment needed ===
[[File:bp1.png|right|200px|thumb|Put a stack of magnets on a reference Miniscope and mark the top magnet to keep track of its polarity]]
[[File:bp2.png|right|200px|thumb|Magnetically attach the top magnet to screwdriver, coat with cyanoacrylate glue on the edge, and push through hole on baseplate]]
[[File:bp3.png|right|200px|thumb|Repeat for remaining two magnets; ensure top of baseplate is completely flat]]
[[File:bp4.png|right|200px|thumb|Coat bottom of baseplate with cyanoacrylate glue]]
[[File:bp5.png|right|200px|thumb|Score bottom and edges of baseplate with a dental drill]]
You will only need basic surgical equipment to baseplate. This includes a mouse stereotax, an isoflurane vaporizer, surgical heat pad, stereo surgical microscope, light source, and a dental drill.

You will also need cyanoacrylate glue, fine forceps, double distilled water, lens paper, and dental cement

=== Baseplate Preparation ===
Before affixing the baseplate on an animal, you will need to prepare the baseplate.
The first step is to insert magnets into the appropriate holes on the baseplate. To ensure that the polarity of the magnets is correct throughout the baseplate preparation, use a reference Miniscope to hold onto the magnets. Mark the top magnet with a sharpie, as seen in the picture to the right. Next, put the top magnet on the head of a screwdriver with the marked side facing away from the screwdriver. Apply cyanoacrylate glue on the edge of the magnet, then push the magnet through the appropriate hole. Ensure that the magnet goes through the hole completely and the top side of the baseplate is flat, as the quality of imaging relies on the Miniscope sitting flush on the baseplate. Repeat this procedure for the next 2 magnets. Finally, put a coat of cyanoacrylate glue on the bottom side of the baseplate and leave the baseplate to dry.
Once the baseplate has dried, score the bottom and the sides of the baseplate using a dental drill to allow the dental glue to adhere the baseplate and skull well.

{{#ev:youtube|https://youtu.be/z_32O2XoYI4|640|center}}

=== Cap Preparation ===
Similar to the baseplate preparation, use a reference Miniscope to hold onto the magnets. Mark the top magnet with a sharpie, and put the magnet on the head of a screwdriver with the marked side facing toward the screwdriver. Coat the magnet with cyanoacrylate glue and push the magnet into the appropriate hole. Repeat for the remaining two magnets.
=== Baseplating ===
Connect a Miniscope to a DAQ and initialize the Miniscope software on a computer. Attach your prepared baseplate onto the bottom of the Miniscope using a set screw.

Using a stereotax and isoflurane vaporizer, anesthetize the animal and fix ear bars until the animal is stable. Carefully remove the Kwik-Sil off the top of the animal’s GRIN lens with blunt forceps being sure not to scratch the lens. Under a stereo surgical microscope, check to see if there is debris on the top of the GRIN lens. If there is, dampen a sheet of lens paper using double distilled water. Wipe the top of the GRIN lens using fine forceps and lens paper, being sure to only wipe laterally and not to apply direct downward pressure.

After the top of the GRIN lens is clean, explore the field of view with the Miniscope. Adjust the LED brightness and focus accordingly. We advise that you use maximum gain and low LED excitation as to not photobleach the brain during baseplating. After finding your ideal view, practice taking the Miniscope off and on and finding the same view.

When you feel comfortable repeatedly finding the view with the Miniscope, apply dental cement in a “C” pattern around the GRIN lens, making sure not to touch the lens itself. It will be easier if your first application of dental cement is more viscous. Put the Miniscope on top of the lens and find your ideal view. Hold the Miniscope steadily as the first application of dental cement dries, making sure that your view does not change.
After the first application of dental cement dries, mix more dental cement and apply it on the posterior edge of the baseplate, making sure it seals to the skull. At this point, you can also build up dental cement along the wall of the baseplate on the animal’s right side. Be sure to avoid applying dental cement onto the camera itself and adhering it to the baseplate. Once the dental cement dries and you feel confident that the baseplate will no longer shift, carefully remove the Miniscope from the baseplate by unscrewing the set screw and lifting it off.

Apply dental cement to the anterior edge of the baseplate and fill in the gaps between the baseplate and skull on the animal’s left side. Allow the dental cement to dry and attach the plastic cap onto the top of the baseplate with a set screw.

{{#ev:youtube|https://youtu.be/GoDJGfqO3po|640|center}}

=== Relay Baseplating ===
If using a relay lens for deep imaging, you have 2 options for baseplating. First, you can secure the large objective GRIN lens into the Miniscope (see [[Imaging With Thin GRIN Lenses]]) and baseplate as you would with a single lens (see video above). Alternatively, you can cement that objective lens onto the animals head in order to make it more stable across imaging sessions. We have found this to be far better for stable recording across weeks. The video below steps through this option and demonstrates how to secure the objective GRIN lens into place while imaging.

{{#ev:youtube|https://youtu.be/b-LrnOBX3j8|640|center}}

Surgery Protocol

2019-10-17T14:51:13Z

Tristanshuman: /* Baseplating Protocol */

The following is a basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging. For videos of surgery and baseplating, see the [[Online Workshop]]. Also, see the recent Nature Protocols paper from the Stuber Lab ([http://www.nature.com/nprot/journal/v11/n3/full/nprot.2016.021.html link]) that has a very detailed description of the surgery.

In order to image, animals will need to undergo three surgical procedures: a virus injection, a GRIN lens implantation, and baseplate attachment.

== Virus Injection ==
Before implanting the GRIN lens, you will need to inject a fluorescent indicator such as GCaMP6. We have generally used AAV1.Syn.GCaMP6f.WPRE.SV40 from Penn Vector (Item number AV-1-PV2822) and had great success in dorsal CA1. You may also be able to use GCaMP6 transgenic mice, but we have not tested whether any of the newer lines are bright enough to be imaged.

== GRIN Lens Implantation==

=== Basic Equipment Needed ===
You will only need basic surgical equipment to perform GRIN lens implantation surgeries. This includes a mouse stereotax, an isoflurane vaporizor, surgical heat pad, stereo surgical microscope, light source, dental drill, and bead sterilizer. For recommended equipment, see the master [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].

You will need the following basic tools and supplies: fine forceps, blunt forceps, fine scissors, scalpel and blade, small skull screws, drill bits, cyanoacrylate glue, dental cement, Kwik-Sil, and [[cortex buffer]]

=== Aspirator and Lens Holder ===
You will need an aspirator to remove cortex above the hippocampus. This can be built very simply with a vacuum line (or pump), a liquid trap, 1 ml syringe (with a hole to control suction), blunt needles, tubing and connectors, and hot glue.
[[File:Aspirator.PNG|center|500px]]

You can easily build a GRIN lens holder by using a suction system to hold the lens in place as it is dropped into the brain for implantation. To build, start with two 1ml micropipette tips. Cut the first so that the tip is just larger than the diameter of the GRIN lens you will be using. Cut the second tip so that the end is just smaller than the size of the GRIN lens. Connect this end to a 1ml syringe and connect to a vacuum line. This will then hold the lens in place during implantation. You can then use tape to attach this holder to a stereotax. Another solution we have used is a basic drill chuck, but this is only good for large (2mm) lenses.
[[File:LensHolder.PNG|center|500px]]

=== Skull Preparation ===
You must first prepare the skull for implantation. We recommend shaving the head area and sterilizing with 3 alternating betadine and ethanol scrubs. Next, remove the scalp with scissors and clean the skull with hydrogen peroxide and saline. Scrape and score the skull to increase the bond with the glue. We also detach the neck muscle from the skull in order to reduce pull on the skull and prevent muscle growth that can make the implant less stable. Finally we insert a skull screw on the opposite side of the skull to enhance the stability of the implant.

=== Craniotomy and Aspiration ===
Using a stereotax, align the skull and find the location for the implant. Using a drill, make 4 guide holes to outline the lens placement. For CA1, we recommend offsetting the lens 0.5mm to the medial side of the virus injection to prevent imaging any damage induced by the virus injection. Connect the guide holes to create a circular craniotomy and peel off the circular skull fragment. Do not worry about blood as the top layers of cortex will be removed by aspiration. Make absolutely sure that the craniotomy is at least the size of your GRIN lens! Cover with cortex buffer and scrape around the outside of the craniotomy to remove any excess bone or dura.

While keeping a constant flow of cortex buffer use the aspirator to slowly remove the cortex above the hippocampus. Continue removing cortex until you reach the white striations of the corpus callosum. Very slowly and carefully remove the horizontal white striations of the corpus callosum until you reach the striations that go vertical. When you reach these striations, stop aspirating and clean up the sides so that the lens can be placed into the brain. Continue washing with cortex buffer until all bleeding stops and keep the brain constantly flushed with cortex buffer.

=== Lens implantation ===
Attach GRIN lens to lens holder on stereotax. Align the lens with the top of the skull at the most posterior part of the craniotomy and quickly insert the lens 1.35 mm below the top of the skull. Remove any excess liquid with the aspirator. Connect the outside of the GRIN lens with the skull and skull screw using cyanoacrylate glue and let fully dry or use a glue accelerator. Remove the lens holder by simply removing the vacuum suction (you can just pinch the tubing) and withdrawing the holder. Next, cover the entire skull with cyanoacrylate glue, and then cover with dental cement. Let dry completely and cover with Kwik-Sil to protect the lens. Remove from stereotax and allow the animal to recover. Give the animal amoxicillin (or equivalent) for 7 days, and daily injections of carprofen and dexamethasone for 7 days.

=== Important tips to remember ===
*Try to keep the surgery as sterile as possible. Infections will destroy imaging and the ability to keep the same cells over many days.

*Try to keep isoflurane as low as possible. Surgeries can take 2-6 hours depending on experience.

*Aspirations will take a lot of practice. Go slow at first.

*Depth will be trial and error. If the first few animals don't give good images, check the depth using histology and adjust accordingly.

Please feel free to add any tips that you have!

== Baseplating Protocol ==

=== Basic Equipment needed ===
[[File:bp1.png|right|200px|thumb|Put a stack of magnets on a reference Miniscope and mark the top magnet to keep track of its polarity]]
[[File:bp2.png|right|200px|thumb|Magnetically attach the top magnet to screwdriver, coat with cyanoacrylate glue on the edge, and push through hole on baseplate]]
[[File:bp3.png|right|200px|thumb|Repeat for remaining two magnets; ensure top of baseplate is completely flat]]
[[File:bp4.png|right|200px|thumb|Coat bottom of baseplate with cyanoacrylate glue]]
[[File:bp5.png|right|200px|thumb|Score bottom and edges of baseplate with a dental drill]]
You will only need basic surgical equipment to baseplate. This includes a mouse stereotax, an isoflurane vaporizer, surgical heat pad, stereo surgical microscope, light source, and a dental drill.

You will also need cyanoacrylate glue, fine forceps, double distilled water, lens paper, and dental cement

=== Baseplate Preparation ===
Before affixing the baseplate on an animal, you will need to prepare the baseplate.
The first step is to insert magnets into the appropriate holes on the baseplate. To ensure that the polarity of the magnets is correct throughout the baseplate preparation, use a reference Miniscope to hold onto the magnets. Mark the top magnet with a sharpie, as seen in the picture to the right. Next, put the top magnet on the head of a screwdriver with the marked side facing away from the screwdriver. Apply cyanoacrylate glue on the edge of the magnet, then push the magnet through the appropriate hole. Ensure that the magnet goes through the hole completely and the top side of the baseplate is flat, as the quality of imaging relies on the Miniscope sitting flush on the baseplate. Repeat this procedure for the next 2 magnets. Finally, put a coat of cyanoacrylate glue on the bottom side of the baseplate and leave the baseplate to dry.
Once the baseplate has dried, score the bottom and the sides of the baseplate using a dental drill to allow the dental glue to adhere the baseplate and skull well.

{{#ev:youtube|https://youtu.be/z_32O2XoYI4|640|center}}

=== Cap Preparation ===
Similar to the baseplate preparation, use a reference Miniscope to hold onto the magnets. Mark the top magnet with a sharpie, and put the magnet on the head of a screwdriver with the marked side facing toward the screwdriver. Coat the magnet with cyanoacrylate glue and push the magnet into the appropriate hole. Repeat for the remaining two magnets.
=== Baseplating ===
Connect a Miniscope to a DAQ and initialize the Miniscope software on a computer. Attach your prepared baseplate onto the bottom of the Miniscope using a set screw.

Using a stereotax and isoflurane vaporizer, anesthetize the animal and fix ear bars until the animal is stable. Carefully remove the Kwik-Sil off the top of the animal’s GRIN lens with blunt forceps being sure not to scratch the lens. Under a stereo surgical microscope, check to see if there is debris on the top of the GRIN lens. If there is, dampen a sheet of lens paper using double distilled water. Wipe the top of the GRIN lens using fine forceps and lens paper, being sure to only wipe laterally and not to apply direct downward pressure.

After the top of the GRIN lens is clean, explore the field of view with the Miniscope. Adjust the LED brightness and focus accordingly. We advise that you use maximum gain and low LED excitation as to not photobleach the brain during baseplating. After finding your ideal view, practice taking the Miniscope off and on and finding the same view.

When you feel comfortable repeatedly finding the view with the Miniscope, apply dental cement in a “C” pattern around the GRIN lens, making sure not to touch the lens itself. It will be easier if your first application of dental cement is more viscous. Put the Miniscope on top of the lens and find your ideal view. Hold the Miniscope steadily as the first application of dental cement dries, making sure that your view does not change.
After the first application of dental cement dries, mix more dental cement and apply it on the posterior edge of the baseplate, making sure it seals to the skull. At this point, you can also build up dental cement along the wall of the baseplate on the animal’s right side. Be sure to avoid applying dental cement onto the camera itself and adhering it to the baseplate. Once the dental cement dries and you feel confident that the baseplate will no longer shift, carefully remove the Miniscope from the baseplate by unscrewing the set screw and lifting it off.

Apply dental cement to the anterior edge of the baseplate and fill in the gaps between the baseplate and skull on the animal’s left side. Allow the dental cement to dry and attach the plastic cap onto the top of the baseplate with a set screw.

{{#ev:youtube|https://youtu.be/GoDJGfqO3po|640|center}}

=== Relay Baseplating ===
If using a relay lens for deep imaging, you have 2 options for baseplating. First, you can secure the large objective GRIN lens into the Miniscope and baseplate as you would with a single lens (see video above). Alternatively, you can cement that objective lens onto the animals head in order to make it more stable across imaging sessions. We have found this to be far better for stable recording across weeks. The video below steps through this option and demonstrates how to secure the objective GRIN lens into place while imaging.

{{#ev:youtube|https://youtu.be/b-LrnOBX3j8|640|center}}

Wire-free Miniscope

2019-05-21T02:44:20Z

Tristanshuman: /* Additional components that may need to be ordered */

== Overview ==
The wire-free Miniscope is a battery powered, data logging Miniscope that is fully untethered from external DAQ and power hardware. This system is a modification to the current wired Miniscope system (version 3.2) and shares all the same components except for the focus slider, CMOS PCB, and DAQ PCB. Below covers everything needed to get up and running with the wire-free Miniscope system.

[[File:Wire-free.PNG|thumb|right|600px|Wire-free schematic and PCB.]]

=== Generally information, notes, and troubleshooting ===
* All design files, source code, firmware, and software can be found [https://github.com/Aharoni-Lab/Documentation-Internal/tree/master/Projects/Wire-Free-Miniscope here].
* The wire-free Miniscope optics are very similar to the v3 Miniscope. You can use the same Miniscope body, cover, baseplates, and magnets. The two systems are completely interchangeable on the animal.
* The wire-free Miniscope's gain, excitation LED power, and recording length is configured on power-up once an microSD card is detected by the on board microcontroller. The microcontroller checks specific memory locations in the microSD card to load the configuration. Configurations are initially uploaded onto the microSD card using our MiniscopeSDCardReader software.
* Once the wire-free Miniscope has been powered up and a microSD card has been detected, the Miniscope waits 5 seconds then begins recording at 20FPS. At the start of recording the red status LED on the wire-free PCB will light up. Once recording has finished the red status LED will turn off. You can use the on and off timing of this LED to synchronize wire-free Minsicope recordings with an external behavioral camera.
* The last 12 pixels values of each frame recorded to the microSD card are over written with a footer that contains four 32bit values. The second to last 32bit value contains the time stamp of that frame. This timestamp is in milliseconds and relative to the start of recording. We have validated that this timestamp is extremely stable across 25 minute recordings. Below is an example code snippet of how you can reconstruct the timestamp for a give frame 'frame' in MATLAB:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

* The wire-free system will run on any single cell lipo battery (and more generally, with anything supplying between 4.2V and 3.4V that is capable of supplying ~80mA). With a 45mAh single cell lipo battery you can expect to get slightly over 20 minutes of recording.
* The suggested workflow is to first image the animals with a wired Miniscope to get an estimate of focal depth, gain, and excitation LED power. Set these parameters on the wire-free Miniscope and then do short recordings, checking the resulting video each time, while adjusting the parameters until you have achieved good imaging. In our experience, once you find the optimal parameters you should be able to keep those same parameters across weeks.

 

== Tutorial on setting up a new wire-free Miniscope ==
=== 1) First we need to make sure we have all the components and software to get things up and running. ===
==== Major new Miniscope components that need to be ordered ====
The wire-free Miniscope uses all the same hardware and optics as the standard v3 Miniscope except for the focus slider and CMOS PCB. It also doesn't use the Miniscope DAQ PCB.
* '''Wire-free Miniscope Focus Slider''': You can get the wire-free focus slider machined by Shylo Stiteler <shylostiteler@gmail.com> or elsewhere. The design file and dimensions are in the "wire-free focus slider" folder in our github repository. When assembling the Miniscope, if the resistors on the PCB prevents the focus slider from fitting in snugly, you can use a scalpel to indent the top of the focus slider.
[[File:MS_FocusSlidervWireless.png|thumb|right|300px|Wire-free focus slider.]]
 
* '''Wire-free Miniscope CMOS PCB''': You will also need the wire-free CMOS PCB. '''''You can order this PCB already programmed and tested along with all the supporting equipment (batteries, connectors, chargers, SD Cards) from Filipe Carvalho <filipe@open-ephys.org>.''''' Of course you can also get this PCB made at your preferred PCB fab/assembly house as well. You can find the fabrication and assembly files in the "wire-free CMOS PCB" folder.
[[File:wire-free-PCB.png|thumb|right|300px|Wire-free PCB.]]
 

==== Additional components that may need to be ordered ====
The list below outlines the additional hardware and tools you need when setting up your own wire-free Miniscope. If you purchase a wire-free Miniscope system from Filipe Carvalho <filipe@open-ephys.org> you won't need the Atmel ICE as the PCB will already come programmed. Also, he can supply SDcards, batteries that are already wired up with the correct connectors, and an open-source lipo charging array with appropriate charge current.

If you are having the wire-free PCB produced somewhere else you will need the following:
* [https://www.digikey.com/products/en?mpart=ATATMEL-ICE&v=150 Atmel ICE] for programming the wire-free PCB
* Micro SD cards. We like to use [https://www.amazon.com/Sandisk-Extreme-MicroSDHC-UHS-I-SDSDQXL-032G-A46A/dp/B00G5R75AU/ref=sr_1_13?s=electronics&ie=UTF8&qid=1543963603&sr=1-13&keywords=sandisk+micro+sd+card+extreme these microSD cards]. The SanDisk microSD extreme cards seem to perform best.
* [https://www.powerstream.com/ultra-light.htm Small Lipo battery]. These 45mAH batteries from Powerstream are cheap, easy and work well. They reliably give just over 20 minutes of recording time. We have also used batteries from [https://www.wyon.ch/en/home.html Wyon]. These batteries are significantly lighter and give longer recording times, but are more expensive and in the past we have had to wait several months to get them. We have had success with their W102 batteries, and are still looking to test their W101 batteries (a bit smaller and lighter).
* Mill-Max 50mil male and female headers. You can get these from digikey.com and they are used to connect the lipo battery and programmer to the CMOS PCB.
* [https://www.sparkfun.com/products/10217 Lipo battery charger]. Most single cell lipo chargers will work. You will need to modify many standard lipo chargers to limit their charging current to what your battery can handle. This is generally done by swapping on a surface mount resistor on the charger PCB (see below).
* [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 50K Resistor]. ~50kOhm 0603 resistors to modify the battery charger.
* [https://www.amazon.com/Tekpower-TP3016M-Portable-Handheld-Variable/dp/B015OA1J82 Power source]. This could be helpful when we are programming and testing the PCB.
* [https://www.amazon.com/AmazonBasics-Male-Micro-Cable-Black/dp/B072J1BSV6/ref=sr_1_1_sspa?crid=19OWZCA50WRE7&keywords=micro+usb+amazon+basics&qid=1555957481&s=gateway&sprefix=micro+usb+amazon+%2Caps%2C337&sr=8-1-spons&psc=1 USB cable]. Micro USB cables to go with the lipo chargers.

==== Software to download ====

* Download [https://mh-nexus.de/en/hxd/ HxD]. This software will allow you to directly edit memory blocks of an SD card which will be needed to initially setup an SD card for wire-free Miniscope recording. '''NOTE''': This software will allow you to modify any byte of data on any drive connected to your computer so observe particular caution when using it.
* Download [https://www.microchip.com/mplab/avr-support/atmel-studio-7 Atmel Studio]. This will be used to program the microcontroller firmware onto the CMOS PCB.
* Download the wire-free Miniscope software found in the "wire-free Miniscope software" folder. This software will allow you to read and save wire-free Miniscope data from an SD card as well as allow you to program recording parameters (exposure, gain, recording length) to the SD card which the Miniscope will read.

=== 2) Now we need to get the wire-free CMOS PCB ready to be programmed with the wire-free Miniscope firmware. ===

==== Soldering the programming header ====
* First solder a 4 pin Mill-Max 50mil pitch header to the 4 pad programming interface on the wire-free CMOS PCB. The connections of this programming header are as follows:

[[File:wire-free-CMOS-PCB-Connections.png|thumb|right|600px|Programming header.]]
 

==== Soldering the lipo battery connector and excitation LED wires ====
* You can also now solder a 2 pin Mill-Max 50mil pitch header and wires for the excitation LED PCB to the three pads near to top of the board in the above picture. First solder the Mill-Max header to Lipo+ and GND (this will be the connector for the lipo battery). Then solder the 2 LED wires to LED+ and the same middle GND pad that the Mill-Max header is soldered to. The CMOS PCB should now look something like this:

[[File:Soldered-PCB-1.png|thumb|right|600px|PCB sensor side.]]

[[File:Soldered-PCB-2.png|thumb|right|600px|PCB sd card side.]]
 

==== Let's also connectorize the Lipo battery ====
* The lipo battery will come with 2 metal strips (initially protected with heat shrink) extending from the body of the battery which are its + and - voltage terminals. We want to solder a wire to each of these metal strips and then put a 2pin Mill-Max header on the other end of the wires so that the battery can connect to the Mill-Max header we soldered to the Lipo+ and GND pads of the CMOS PCB.
[[File:lipo-battery.png|thumb|right|600px|Lipo Battery.]]
 

* Make sure to never short the 2 metal strips of the lipo battery. If you do, it could damage the battery permanently.
* Use a multimeter to test which metal strip is the + and which is the - (GND).
* When soldering wires to the lipo, try to minimize the amount of heat traveling to the lipo battery.

=== 3) Programming the wire-free CMOS PCB ===
==== Connectorizing the Atmel ICE programmer ====
* In order to program the microcontroller on the CMOS PCB, we first need to wire-up and connectorize a 4pin Mill-Max header to the 4 programming pins of the Atmel ICE programmer. These are GND, VTG, SWDIO, and SWDCLK. Below shows which pins/wires of the Atmel ICE have which function. The Atmel ICE has 2 different 5x2 pin ports. One is labeled AVR and one is labeled SAM. Either will work but depending on which one you are using it will change which column you refer to in the below chart.

[[File:atmel-ice-swd-pinout.png|thumb|right|600px|Chart]]
 

* Connect the Atmel ICE to the programming header of the CMOS PCB.
* Power up the CMOS PCB through the lipo connector (2pin Mill-Max head with Lipo+ and GND). You can hook up a charged lipo battery but we suggest using a power supply between 3.5V and 4.2V here. This way you don't have to worry about a battery running out of charge during programming and testing. You can cap the maximum current output of the power source at 0.150A just to be safe. The power source should measure a current of about 0.03A when 3.8V is supplied to the PCB.
* When the CMOS PCB gets powered on, you should see an orange light turn on on the Atmel ICE which shows that the Atmel ICE has detected voltage on the VTG (Voltage Target) pin. In the ATATMEL-ICE-ND, you should see a red light turn on showing that the Atmel box is powered, and a green light showing that the box is measuring a voltage from the PCB. Updating Atmel Studio and restarting the computer could all help with debugging.
* Open Atmel Studio and click the "Device Programming" button

[[File:Atmel-device-programming.PNG|thumb|right|600px|Atmel Studio device programming button.]]
 

* In the Device Programming window that pops up select:
** Tool: Atmel ICE
** Device: ATSAM.... (should automatically be the correct name, ATSAME70N21)
** Interface: SWD
** Then click "Apply"
* Now check to make sure that Atmel Studio can communicate with the microcontroller on the CMOS PCB. You do this by clicking the "Read" button under Device Signature. If everything is powered and connected correctly you should see some numbers and letter pop up in the box and no error window show up. Now we are ready to program the microcontroller.

[[File:device-programming-window.PNG|thumb|right|600px|device programming window.]]
 

* Click "Memory" on the left menu panel of the Device Programming window we are currently in. If the memory tab is not showing up, make sure to select the tool, device, and interface and click apply again
* Click "Browse" and locate the wire-free Miniscope firmware. This is a .hex file you can find in the "/wire-free-firmware" folder. Either the .hex or .elf file should work.
* Click "Program". This will erase, program, and verify the microcontroller. It will tell you if everything was successful.
* Exit the Device Programming window.
* Now we have to do something a bit weird. I am not sure why this has to be done but it does. Open up the Atmel project found in the "/wire-free-firmware" folder. This load up the code that makes up the wire-free Miniscope firmware. Now click "Debug" from the top menu bar and then click "Start Debugging and Break". Wait about 15 seconds while the debugger does its thing in Atmel Studio and then the code should jump to the "main()" function and highlight it. Now click the play button (labelled "Start Debugging") in the top menu. Wait a few seconds then click the stop button (labelled "Stop Debugging").
[[File:loadingATMEL.PNG|thumb|right|600px|Loading Atmel.]]

[[File:ddebug-buttons.PNG|thumb|right|600px|Debug buttons.]]
 
* Go back to the "Device Programming" window by clicking the "Device Programming" button.
* Repeat the steps to program the PCB with the .hex file.
* Now the microcontroller on the wire-free Miniscope CMOS PCB knows how to be a wire-free Miniscope microcontroller.

=== 4) Configure the micro SD card ===
The wire-free Miniscope and the Miniscope SD Card Reader software are able to read and write raw data directly into and out of the memory blocks of the SD card. In memory block 1023 of the SD card, we need to first write an a key that will, for all subsequnt writing to the SD card, be checked before any raw data writed to make sure we are not writing to the wrong drive. '''If we accidently write over a memory block on your computer's drive it can corrupt Windows so we need to be extra careful not to do that.'''

==== Add the Write Key to memory block 1023 of the SD Card ====
Here we will use the HxD software to directly write our Key into the SD Card.
* Open the HxD software and run as Administrator
* Select 'Tools' then select 'Open Disk' from the drop down menu
* Uncheck the 'Open as Readonly' option in the bottom left of the window, select the SD card from the list of disks, and then click 'OK'. If the disk is not showing up, restarting the computer might help.

[[File:HxD1.PNG|thumb|right|600px|HxD.]]
 

* '''We will now be writing directly to memory blocks of the drive. Make sure you have selected the SD Card and not another drive'''
* Go to Sector 1023 and modify the first 16 bytes in this sector.We will be replacing the data in these 16 bytes with the write Key. The write Key is 0x0D7CBA17 repeated 4 times. After replacing these bytes it should look like this:
[[File:HxD2.PNG|thumb|right|600px|HxD write key.]]
 

* Now click 'Save'.
* Let's check to make sure everything was modified and saved correctly. Close HxD, pull out the SD card from the computer and then place it back in the computer. Now open up HxD, open the SD Card disk, go to sector 1023, and check to make sure the write Key is still there. If it is then we have correctly configured the SD Card for wire-free Miniscope recording.

=== 5) Using the Miniscope SD Card Reader software ===
Our final step is to use the Miniscope SD Card Reader software to configure the LED power and Gain of the wire-free Miniscope. The way we do this is by writing the configuration into specific bytes of memory block 1023 of the SD card. The Miniscope SD Card Reader software handles all of this through a simple GUI.
* Open the MiniscopeSDCardReader.exe and run as Administrator
[[File:MiniscopeSDCardReader.PNG|thumb|right|600px|Miniscope SD Card Reader.]]
 
* You may need to change the 'Drive' name based on the naming your computer has given to the SD Card. In the image above it has defaulted to 'PhysicalDrive1' and this name should usually work. If a window pops up asking if you want to format the SD card, do not format it or it will undo what we programmed.
* You can set the Gain, LED Power, and Recording Length. Once the correct numbers have been entered, click 'Set' to write those values to the SD card. The software makes sure the write Key is present in memory block 1023 before attempting to write this configuration. This is used to stop the software from writing to another disk but still be careful. A line should pop up in the bottom window saying “Write key match!”
* After setting the configuration you can take out the SD card from the computer and mount it in the wire-free Miniscope. Once the Miniscope is powered on, it will wait 5 seconds and then begin recording. Always put in the SD card before plugging in the battery.
* After recording with the Miniscope, take the SD card out of the Miniscope mount and place it in your computer. You can now use the MiniscopeSDCardReader software to view, save, and delete recordings.

=== 6) Modifying the Lipo charger ===
In general any single cell lipo charger will work for charging the batteries used for the wire-free Miniscope but you have to make sure that the max current the charge can output is limited to around 20mA. The Sparkfun Lipo charger listed at the top of this tutorial is capped at 500mA by default so we will need to modify the charger to limit the current to ~20mA. The way we do this is by replacing the SMD resistor circled in blue below with a ~50kOhm 0603 resistor. If you don't have a ~50kohn resistor on hand you can [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 order one from digikey]. If the solder around the resistor is hard to remove, it might help to add a little bit of new solder.

[[File:SparkfunChargerMod.png|thumb|right|600px|Sparkfun modified charger.]]
 

You will also need to modify or swap out the lipo connector on the right of the board with connector that can mate to the connector you put on your lipo batteries.

== How to record with the wire-free Miniscope system ==
After following the wire-free Miniscope tutorial above you should now be ready to record using the system. Imaging using the wire-free Miniscope has a few extra steps compared to the wired Miniscope but you set up a workflow for recording the system is often times easier to use than the wired one.

=== Steps for imaging in a unrestrained animal ===
# Use a wired Miniscope to get a ballpark idea of focal depth and excitation power needed for a specific animal.
# Set the focal height of the wire-free Miniscope as close as possible to the wired Miniscope you used in step 1.
# Using the MiniscopeSDCardReader software, set the Gain, LED Power, and recording length. We suggest using a ~5second recording length when first figuring out these settings. This will allow you to quickly image and then check the recording.
[[File:MiniscopeSDCardReader2.png|thumb|right|600px|Settings.]]
 
# Now that you have the focal depth set as well as the gain and LED power figured out, you are ready for your experiment. Mount the wire-free Miniscope on the baseplate on the animal's head.
# Place a microSD card in the SD card mount on the wire-free Miniscope PCB.
# Plug in a '''fully charged''' single cell lipo.
# The wire-free Miniscope will now power up and detect the SD card. You can also power up the Miniscope before mounting the SD card but we have found this to be slightly less stable than the other way around. '''The Miniscope will wait exactly 5 seconds''' before turning on its red status LED and beginning recording.
# The Miniscope will now record for the recording length you previously set through the MiniscopeSDCardReader software. Once the recording has finished the red status LED will turn off. Unplug the lipo battery then remove the SD card.
# Imaging data is stored in a raw format on the SD card. There are no files or folder structures on the SD card. The recording begins in memory block 1024 and will continue until the end of the recording is reached.

=== Steps for transferring a recording from an SD Card to a computer ===
Now that you have a wire-free Miniscope stored on an SD Card, we need to transfer it to a computer. As mentioned above, the wire-free Miniscope records raw pixel byte values directly to memory blocks in the SD Card. This means that when the card is mounted in a computer, the computer will think that the card needs to be reformatted. This is due to the SD Card not having a file system on it. '''Always ignore the recommendation of your computer to reformat the SD Card as well as if it says the SD Card is corrupted.'''
# Mount the SD Card in your computer. If you computer doesn't have a built in SD Card mount, you can use an external USB SD Card mount.
# Open the MiniscopeSDCardReader software in with Administrator privileges. You will need this since we will be directly reading/writing memory blocks.
## The "Drive" is the name of the SD Card. This defaults to "PhysicalDrive1" but you should double check you are using the correct name of the SD Card drive.
## The "Starting Sector" is the memory block where the beginning of the Miniscope recording is located. This should not need to ever be changed from "1024".
## '''Note''': Whenever this software attempts to access data on the SD Card, it first checks to make sure the correct 128bit "WRITE KEY" is stored in memory block 1023. This WRITE KEY was placed there by you if you followed the tutorial above. The goal of this WRITE KEY is it makes it extremely unlikely that you end up accessing or modifying any other drive on your computer since the chances of another drive having the 128bit WRITE KEY located at memory block 1023 is highly unlikely. When you do try accessing data on the SD Card, the text box at the bottom of the GUI will tell you if it found the correct WRITE KEY or if it found the wrong one and stopped the requested action.
# Now you can use the "Read/Save Data" portion of the software to do exactly that... read and/or save the wire-free Miniscope data.
## First enter in the length of the recording you want to extract from the SD Card. This says "Number of Seconds" but I think it is actually "Number of Frames" (''I will get around to fixing this sometime soon...''). The wire-free Miniscope records at 20FPS so you should usually just set this number a bit longer than the expected recording to make sure you grab all the data.
## If you click "Read" the software will open up a window that will play the wire-free Miniscope recording. On some computers using some versions of OpenCV, this option for some reason doesn't actually update the window and it just shows black the whole time. We recommend to use "Save" in all cases if this happens to you.
## If you click "Save" the software will display the video as it extracts it from the SD Card and writes it to the computer's drive. It will save a copy of the wire-free recording in the "data" folder located where ever your MiniscopeSDCardReader software is located. We generally recommend you using the "Save" option over the "Read" option since the read option can be buggy on some computers.
# Check to make sure the data is now saved as an uncompressed .avi file on your computer.
# Once you have your data transferred to your computer we highly recommend clearing the SD Card before beginning a new recording:
## You can do this using the "Clear SD Card" section of the software. Here you can define the number of frames to clear from the SD card and then clear/delete them.
## Set the number of frames to clear first. We suggest entering a number that is larger than the expected length of recording currently on the SD Card.
## Click "Delete" and the software will set all bytes in these memory block in the SD Card to 0.
## '''Note''': It will not delete the settings located in memory block 1023. This means you can now reuse this SD Card without reprogramming the gain, LED power, and recording length.
# '''Note''': Each frame is timestamped and the timestamp is embedded within each frame. You can extract the timestamp by generating a 32bit integer from the last 8th, 7th, 6th, and 5th pixels in each frame. In MATLAB it would look something like this for a given frame:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

You're Done!

Wire-free Miniscope

2019-05-21T02:43:29Z

Tristanshuman: /* Additional components that may need to be ordered */

== Overview ==
The wire-free Miniscope is a battery powered, data logging Miniscope that is fully untethered from external DAQ and power hardware. This system is a modification to the current wired Miniscope system (version 3.2) and shares all the same components except for the focus slider, CMOS PCB, and DAQ PCB. Below covers everything needed to get up and running with the wire-free Miniscope system.

[[File:Wire-free.PNG|thumb|right|600px|Wire-free schematic and PCB.]]

=== Generally information, notes, and troubleshooting ===
* All design files, source code, firmware, and software can be found [https://github.com/Aharoni-Lab/Documentation-Internal/tree/master/Projects/Wire-Free-Miniscope here].
* The wire-free Miniscope optics are very similar to the v3 Miniscope. You can use the same Miniscope body, cover, baseplates, and magnets. The two systems are completely interchangeable on the animal.
* The wire-free Miniscope's gain, excitation LED power, and recording length is configured on power-up once an microSD card is detected by the on board microcontroller. The microcontroller checks specific memory locations in the microSD card to load the configuration. Configurations are initially uploaded onto the microSD card using our MiniscopeSDCardReader software.
* Once the wire-free Miniscope has been powered up and a microSD card has been detected, the Miniscope waits 5 seconds then begins recording at 20FPS. At the start of recording the red status LED on the wire-free PCB will light up. Once recording has finished the red status LED will turn off. You can use the on and off timing of this LED to synchronize wire-free Minsicope recordings with an external behavioral camera.
* The last 12 pixels values of each frame recorded to the microSD card are over written with a footer that contains four 32bit values. The second to last 32bit value contains the time stamp of that frame. This timestamp is in milliseconds and relative to the start of recording. We have validated that this timestamp is extremely stable across 25 minute recordings. Below is an example code snippet of how you can reconstruct the timestamp for a give frame 'frame' in MATLAB:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

* The wire-free system will run on any single cell lipo battery (and more generally, with anything supplying between 4.2V and 3.4V that is capable of supplying ~80mA). With a 45mAh single cell lipo battery you can expect to get slightly over 20 minutes of recording.
* The suggested workflow is to first image the animals with a wired Miniscope to get an estimate of focal depth, gain, and excitation LED power. Set these parameters on the wire-free Miniscope and then do short recordings, checking the resulting video each time, while adjusting the parameters until you have achieved good imaging. In our experience, once you find the optimal parameters you should be able to keep those same parameters across weeks.

 

== Tutorial on setting up a new wire-free Miniscope ==
=== 1) First we need to make sure we have all the components and software to get things up and running. ===
==== Major new Miniscope components that need to be ordered ====
The wire-free Miniscope uses all the same hardware and optics as the standard v3 Miniscope except for the focus slider and CMOS PCB. It also doesn't use the Miniscope DAQ PCB.
* '''Wire-free Miniscope Focus Slider''': You can get the wire-free focus slider machined by Shylo Stiteler <shylostiteler@gmail.com> or elsewhere. The design file and dimensions are in the "wire-free focus slider" folder in our github repository. When assembling the Miniscope, if the resistors on the PCB prevents the focus slider from fitting in snugly, you can use a scalpel to indent the top of the focus slider.
[[File:MS_FocusSlidervWireless.png|thumb|right|300px|Wire-free focus slider.]]
 
* '''Wire-free Miniscope CMOS PCB''': You will also need the wire-free CMOS PCB. '''''You can order this PCB already programmed and tested along with all the supporting equipment (batteries, connectors, chargers, SD Cards) from Filipe Carvalho <filipe@open-ephys.org>.''''' Of course you can also get this PCB made at your preferred PCB fab/assembly house as well. You can find the fabrication and assembly files in the "wire-free CMOS PCB" folder.
[[File:wire-free-PCB.png|thumb|right|300px|Wire-free PCB.]]
 

==== Additional components that may need to be ordered ====
The list below outlines the additional hardware and tools you need when setting up your own wire-free Miniscope. If you purchase a wire-free Miniscope system from Filipe Carvalho <filipe@open-ephys.org> you won't need the Atmel ICE as the PCB will already come programmed. Also, he can supply SDcards, batteries that are already wired up with the correct connectors, and an open-source lipo charging array with appropriate charge current.

If you are having the wire-free PCB produced somewhere else you will need the following:
* [https://www.digikey.com/products/en?mpart=ATATMEL-ICE&v=150 Atmel ICE] for programming the wire-free PCB
* Micro SD cards. We like to use [https://www.amazon.com/Sandisk-Extreme-MicroSDHC-UHS-I-SDSDQXL-032G-A46A/dp/B00G5R75AU/ref=sr_1_13?s=electronics&ie=UTF8&qid=1543963603&sr=1-13&keywords=sandisk+micro+sd+card+extreme these microSD cards]. The SanDisk microSD extreme cards seem to perform best.
* [https://www.powerstream.com/ultra-light.htm Small Lipo battery]. These 45mAH batteries from Powerstream are cheap, easy and work well. They reliably give just over 20 minutes of recording time. We have also used batteries from [https://www.wyon.ch/en/home.html Wyon]. These batteries are significantly lighter and give longer recording times, but are more expensive and in the past we have had to wait several months to get them. We have had success with their W102 batteries, and are still looking to test their W101 batteries (a bit smaller and lighter).
* Mill-Max 50mil male and female headers. You can get these from digikey.com and they are used to connect the lipo battery and programmer to the CMOS PCB.
* [https://www.sparkfun.com/products/10217 Lipo battery charger]. Most single cell lipo chargers will work. You will need to modify many standard lipo chargers to limit their charging current to what your battery can handle. This is generally done by swapping on a surface mount resistor on the charger PCB.
* [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 50K Resistor]. ~50kOhm 0603 resistors to modify the battery charger.
* [https://www.amazon.com/Tekpower-TP3016M-Portable-Handheld-Variable/dp/B015OA1J82 Power source]. This could be helpful when we are programming and testing the PCB.
* [https://www.amazon.com/AmazonBasics-Male-Micro-Cable-Black/dp/B072J1BSV6/ref=sr_1_1_sspa?crid=19OWZCA50WRE7&keywords=micro+usb+amazon+basics&qid=1555957481&s=gateway&sprefix=micro+usb+amazon+%2Caps%2C337&sr=8-1-spons&psc=1 USB cable]. Micro USB cables to go with the lipo chargers.

==== Software to download ====

* Download [https://mh-nexus.de/en/hxd/ HxD]. This software will allow you to directly edit memory blocks of an SD card which will be needed to initially setup an SD card for wire-free Miniscope recording. '''NOTE''': This software will allow you to modify any byte of data on any drive connected to your computer so observe particular caution when using it.
* Download [https://www.microchip.com/mplab/avr-support/atmel-studio-7 Atmel Studio]. This will be used to program the microcontroller firmware onto the CMOS PCB.
* Download the wire-free Miniscope software found in the "wire-free Miniscope software" folder. This software will allow you to read and save wire-free Miniscope data from an SD card as well as allow you to program recording parameters (exposure, gain, recording length) to the SD card which the Miniscope will read.

=== 2) Now we need to get the wire-free CMOS PCB ready to be programmed with the wire-free Miniscope firmware. ===

==== Soldering the programming header ====
* First solder a 4 pin Mill-Max 50mil pitch header to the 4 pad programming interface on the wire-free CMOS PCB. The connections of this programming header are as follows:

[[File:wire-free-CMOS-PCB-Connections.png|thumb|right|600px|Programming header.]]
 

==== Soldering the lipo battery connector and excitation LED wires ====
* You can also now solder a 2 pin Mill-Max 50mil pitch header and wires for the excitation LED PCB to the three pads near to top of the board in the above picture. First solder the Mill-Max header to Lipo+ and GND (this will be the connector for the lipo battery). Then solder the 2 LED wires to LED+ and the same middle GND pad that the Mill-Max header is soldered to. The CMOS PCB should now look something like this:

[[File:Soldered-PCB-1.png|thumb|right|600px|PCB sensor side.]]

[[File:Soldered-PCB-2.png|thumb|right|600px|PCB sd card side.]]
 

==== Let's also connectorize the Lipo battery ====
* The lipo battery will come with 2 metal strips (initially protected with heat shrink) extending from the body of the battery which are its + and - voltage terminals. We want to solder a wire to each of these metal strips and then put a 2pin Mill-Max header on the other end of the wires so that the battery can connect to the Mill-Max header we soldered to the Lipo+ and GND pads of the CMOS PCB.
[[File:lipo-battery.png|thumb|right|600px|Lipo Battery.]]
 

* Make sure to never short the 2 metal strips of the lipo battery. If you do, it could damage the battery permanently.
* Use a multimeter to test which metal strip is the + and which is the - (GND).
* When soldering wires to the lipo, try to minimize the amount of heat traveling to the lipo battery.

=== 3) Programming the wire-free CMOS PCB ===
==== Connectorizing the Atmel ICE programmer ====
* In order to program the microcontroller on the CMOS PCB, we first need to wire-up and connectorize a 4pin Mill-Max header to the 4 programming pins of the Atmel ICE programmer. These are GND, VTG, SWDIO, and SWDCLK. Below shows which pins/wires of the Atmel ICE have which function. The Atmel ICE has 2 different 5x2 pin ports. One is labeled AVR and one is labeled SAM. Either will work but depending on which one you are using it will change which column you refer to in the below chart.

[[File:atmel-ice-swd-pinout.png|thumb|right|600px|Chart]]
 

* Connect the Atmel ICE to the programming header of the CMOS PCB.
* Power up the CMOS PCB through the lipo connector (2pin Mill-Max head with Lipo+ and GND). You can hook up a charged lipo battery but we suggest using a power supply between 3.5V and 4.2V here. This way you don't have to worry about a battery running out of charge during programming and testing. You can cap the maximum current output of the power source at 0.150A just to be safe. The power source should measure a current of about 0.03A when 3.8V is supplied to the PCB.
* When the CMOS PCB gets powered on, you should see an orange light turn on on the Atmel ICE which shows that the Atmel ICE has detected voltage on the VTG (Voltage Target) pin. In the ATATMEL-ICE-ND, you should see a red light turn on showing that the Atmel box is powered, and a green light showing that the box is measuring a voltage from the PCB. Updating Atmel Studio and restarting the computer could all help with debugging.
* Open Atmel Studio and click the "Device Programming" button

[[File:Atmel-device-programming.PNG|thumb|right|600px|Atmel Studio device programming button.]]
 

* In the Device Programming window that pops up select:
** Tool: Atmel ICE
** Device: ATSAM.... (should automatically be the correct name, ATSAME70N21)
** Interface: SWD
** Then click "Apply"
* Now check to make sure that Atmel Studio can communicate with the microcontroller on the CMOS PCB. You do this by clicking the "Read" button under Device Signature. If everything is powered and connected correctly you should see some numbers and letter pop up in the box and no error window show up. Now we are ready to program the microcontroller.

[[File:device-programming-window.PNG|thumb|right|600px|device programming window.]]
 

* Click "Memory" on the left menu panel of the Device Programming window we are currently in. If the memory tab is not showing up, make sure to select the tool, device, and interface and click apply again
* Click "Browse" and locate the wire-free Miniscope firmware. This is a .hex file you can find in the "/wire-free-firmware" folder. Either the .hex or .elf file should work.
* Click "Program". This will erase, program, and verify the microcontroller. It will tell you if everything was successful.
* Exit the Device Programming window.
* Now we have to do something a bit weird. I am not sure why this has to be done but it does. Open up the Atmel project found in the "/wire-free-firmware" folder. This load up the code that makes up the wire-free Miniscope firmware. Now click "Debug" from the top menu bar and then click "Start Debugging and Break". Wait about 15 seconds while the debugger does its thing in Atmel Studio and then the code should jump to the "main()" function and highlight it. Now click the play button (labelled "Start Debugging") in the top menu. Wait a few seconds then click the stop button (labelled "Stop Debugging").
[[File:loadingATMEL.PNG|thumb|right|600px|Loading Atmel.]]

[[File:ddebug-buttons.PNG|thumb|right|600px|Debug buttons.]]
 
* Go back to the "Device Programming" window by clicking the "Device Programming" button.
* Repeat the steps to program the PCB with the .hex file.
* Now the microcontroller on the wire-free Miniscope CMOS PCB knows how to be a wire-free Miniscope microcontroller.

=== 4) Configure the micro SD card ===
The wire-free Miniscope and the Miniscope SD Card Reader software are able to read and write raw data directly into and out of the memory blocks of the SD card. In memory block 1023 of the SD card, we need to first write an a key that will, for all subsequnt writing to the SD card, be checked before any raw data writed to make sure we are not writing to the wrong drive. '''If we accidently write over a memory block on your computer's drive it can corrupt Windows so we need to be extra careful not to do that.'''

==== Add the Write Key to memory block 1023 of the SD Card ====
Here we will use the HxD software to directly write our Key into the SD Card.
* Open the HxD software and run as Administrator
* Select 'Tools' then select 'Open Disk' from the drop down menu
* Uncheck the 'Open as Readonly' option in the bottom left of the window, select the SD card from the list of disks, and then click 'OK'. If the disk is not showing up, restarting the computer might help.

[[File:HxD1.PNG|thumb|right|600px|HxD.]]
 

* '''We will now be writing directly to memory blocks of the drive. Make sure you have selected the SD Card and not another drive'''
* Go to Sector 1023 and modify the first 16 bytes in this sector.We will be replacing the data in these 16 bytes with the write Key. The write Key is 0x0D7CBA17 repeated 4 times. After replacing these bytes it should look like this:
[[File:HxD2.PNG|thumb|right|600px|HxD write key.]]
 

* Now click 'Save'.
* Let's check to make sure everything was modified and saved correctly. Close HxD, pull out the SD card from the computer and then place it back in the computer. Now open up HxD, open the SD Card disk, go to sector 1023, and check to make sure the write Key is still there. If it is then we have correctly configured the SD Card for wire-free Miniscope recording.

=== 5) Using the Miniscope SD Card Reader software ===
Our final step is to use the Miniscope SD Card Reader software to configure the LED power and Gain of the wire-free Miniscope. The way we do this is by writing the configuration into specific bytes of memory block 1023 of the SD card. The Miniscope SD Card Reader software handles all of this through a simple GUI.
* Open the MiniscopeSDCardReader.exe and run as Administrator
[[File:MiniscopeSDCardReader.PNG|thumb|right|600px|Miniscope SD Card Reader.]]
 
* You may need to change the 'Drive' name based on the naming your computer has given to the SD Card. In the image above it has defaulted to 'PhysicalDrive1' and this name should usually work. If a window pops up asking if you want to format the SD card, do not format it or it will undo what we programmed.
* You can set the Gain, LED Power, and Recording Length. Once the correct numbers have been entered, click 'Set' to write those values to the SD card. The software makes sure the write Key is present in memory block 1023 before attempting to write this configuration. This is used to stop the software from writing to another disk but still be careful. A line should pop up in the bottom window saying “Write key match!”
* After setting the configuration you can take out the SD card from the computer and mount it in the wire-free Miniscope. Once the Miniscope is powered on, it will wait 5 seconds and then begin recording. Always put in the SD card before plugging in the battery.
* After recording with the Miniscope, take the SD card out of the Miniscope mount and place it in your computer. You can now use the MiniscopeSDCardReader software to view, save, and delete recordings.

=== 6) Modifying the Lipo charger ===
In general any single cell lipo charger will work for charging the batteries used for the wire-free Miniscope but you have to make sure that the max current the charge can output is limited to around 20mA. The Sparkfun Lipo charger listed at the top of this tutorial is capped at 500mA by default so we will need to modify the charger to limit the current to ~20mA. The way we do this is by replacing the SMD resistor circled in blue below with a ~50kOhm 0603 resistor. If you don't have a ~50kohn resistor on hand you can [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 order one from digikey]. If the solder around the resistor is hard to remove, it might help to add a little bit of new solder.

[[File:SparkfunChargerMod.png|thumb|right|600px|Sparkfun modified charger.]]
 

You will also need to modify or swap out the lipo connector on the right of the board with connector that can mate to the connector you put on your lipo batteries.

== How to record with the wire-free Miniscope system ==
After following the wire-free Miniscope tutorial above you should now be ready to record using the system. Imaging using the wire-free Miniscope has a few extra steps compared to the wired Miniscope but you set up a workflow for recording the system is often times easier to use than the wired one.

=== Steps for imaging in a unrestrained animal ===
# Use a wired Miniscope to get a ballpark idea of focal depth and excitation power needed for a specific animal.
# Set the focal height of the wire-free Miniscope as close as possible to the wired Miniscope you used in step 1.
# Using the MiniscopeSDCardReader software, set the Gain, LED Power, and recording length. We suggest using a ~5second recording length when first figuring out these settings. This will allow you to quickly image and then check the recording.
[[File:MiniscopeSDCardReader2.png|thumb|right|600px|Settings.]]
 
# Now that you have the focal depth set as well as the gain and LED power figured out, you are ready for your experiment. Mount the wire-free Miniscope on the baseplate on the animal's head.
# Place a microSD card in the SD card mount on the wire-free Miniscope PCB.
# Plug in a '''fully charged''' single cell lipo.
# The wire-free Miniscope will now power up and detect the SD card. You can also power up the Miniscope before mounting the SD card but we have found this to be slightly less stable than the other way around. '''The Miniscope will wait exactly 5 seconds''' before turning on its red status LED and beginning recording.
# The Miniscope will now record for the recording length you previously set through the MiniscopeSDCardReader software. Once the recording has finished the red status LED will turn off. Unplug the lipo battery then remove the SD card.
# Imaging data is stored in a raw format on the SD card. There are no files or folder structures on the SD card. The recording begins in memory block 1024 and will continue until the end of the recording is reached.

=== Steps for transferring a recording from an SD Card to a computer ===
Now that you have a wire-free Miniscope stored on an SD Card, we need to transfer it to a computer. As mentioned above, the wire-free Miniscope records raw pixel byte values directly to memory blocks in the SD Card. This means that when the card is mounted in a computer, the computer will think that the card needs to be reformatted. This is due to the SD Card not having a file system on it. '''Always ignore the recommendation of your computer to reformat the SD Card as well as if it says the SD Card is corrupted.'''
# Mount the SD Card in your computer. If you computer doesn't have a built in SD Card mount, you can use an external USB SD Card mount.
# Open the MiniscopeSDCardReader software in with Administrator privileges. You will need this since we will be directly reading/writing memory blocks.
## The "Drive" is the name of the SD Card. This defaults to "PhysicalDrive1" but you should double check you are using the correct name of the SD Card drive.
## The "Starting Sector" is the memory block where the beginning of the Miniscope recording is located. This should not need to ever be changed from "1024".
## '''Note''': Whenever this software attempts to access data on the SD Card, it first checks to make sure the correct 128bit "WRITE KEY" is stored in memory block 1023. This WRITE KEY was placed there by you if you followed the tutorial above. The goal of this WRITE KEY is it makes it extremely unlikely that you end up accessing or modifying any other drive on your computer since the chances of another drive having the 128bit WRITE KEY located at memory block 1023 is highly unlikely. When you do try accessing data on the SD Card, the text box at the bottom of the GUI will tell you if it found the correct WRITE KEY or if it found the wrong one and stopped the requested action.
# Now you can use the "Read/Save Data" portion of the software to do exactly that... read and/or save the wire-free Miniscope data.
## First enter in the length of the recording you want to extract from the SD Card. This says "Number of Seconds" but I think it is actually "Number of Frames" (''I will get around to fixing this sometime soon...''). The wire-free Miniscope records at 20FPS so you should usually just set this number a bit longer than the expected recording to make sure you grab all the data.
## If you click "Read" the software will open up a window that will play the wire-free Miniscope recording. On some computers using some versions of OpenCV, this option for some reason doesn't actually update the window and it just shows black the whole time. We recommend to use "Save" in all cases if this happens to you.
## If you click "Save" the software will display the video as it extracts it from the SD Card and writes it to the computer's drive. It will save a copy of the wire-free recording in the "data" folder located where ever your MiniscopeSDCardReader software is located. We generally recommend you using the "Save" option over the "Read" option since the read option can be buggy on some computers.
# Check to make sure the data is now saved as an uncompressed .avi file on your computer.
# Once you have your data transferred to your computer we highly recommend clearing the SD Card before beginning a new recording:
## You can do this using the "Clear SD Card" section of the software. Here you can define the number of frames to clear from the SD card and then clear/delete them.
## Set the number of frames to clear first. We suggest entering a number that is larger than the expected length of recording currently on the SD Card.
## Click "Delete" and the software will set all bytes in these memory block in the SD Card to 0.
## '''Note''': It will not delete the settings located in memory block 1023. This means you can now reuse this SD Card without reprogramming the gain, LED power, and recording length.
# '''Note''': Each frame is timestamped and the timestamp is embedded within each frame. You can extract the timestamp by generating a 32bit integer from the last 8th, 7th, 6th, and 5th pixels in each frame. In MATLAB it would look something like this for a given frame:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

You're Done!

Wire-free Miniscope

2019-05-21T02:37:17Z

Tristanshuman: /* Generally information, notes, and troubleshooting */

== Overview ==
The wire-free Miniscope is a battery powered, data logging Miniscope that is fully untethered from external DAQ and power hardware. This system is a modification to the current wired Miniscope system (version 3.2) and shares all the same components except for the focus slider, CMOS PCB, and DAQ PCB. Below covers everything needed to get up and running with the wire-free Miniscope system.

[[File:Wire-free.PNG|thumb|right|600px|Wire-free schematic and PCB.]]

=== Generally information, notes, and troubleshooting ===
* All design files, source code, firmware, and software can be found [https://github.com/Aharoni-Lab/Documentation-Internal/tree/master/Projects/Wire-Free-Miniscope here].
* The wire-free Miniscope optics are very similar to the v3 Miniscope. You can use the same Miniscope body, cover, baseplates, and magnets. The two systems are completely interchangeable on the animal.
* The wire-free Miniscope's gain, excitation LED power, and recording length is configured on power-up once an microSD card is detected by the on board microcontroller. The microcontroller checks specific memory locations in the microSD card to load the configuration. Configurations are initially uploaded onto the microSD card using our MiniscopeSDCardReader software.
* Once the wire-free Miniscope has been powered up and a microSD card has been detected, the Miniscope waits 5 seconds then begins recording at 20FPS. At the start of recording the red status LED on the wire-free PCB will light up. Once recording has finished the red status LED will turn off. You can use the on and off timing of this LED to synchronize wire-free Minsicope recordings with an external behavioral camera.
* The last 12 pixels values of each frame recorded to the microSD card are over written with a footer that contains four 32bit values. The second to last 32bit value contains the time stamp of that frame. This timestamp is in milliseconds and relative to the start of recording. We have validated that this timestamp is extremely stable across 25 minute recordings. Below is an example code snippet of how you can reconstruct the timestamp for a give frame 'frame' in MATLAB:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

* The wire-free system will run on any single cell lipo battery (and more generally, with anything supplying between 4.2V and 3.4V that is capable of supplying ~80mA). With a 45mAh single cell lipo battery you can expect to get slightly over 20 minutes of recording.
* The suggested workflow is to first image the animals with a wired Miniscope to get an estimate of focal depth, gain, and excitation LED power. Set these parameters on the wire-free Miniscope and then do short recordings, checking the resulting video each time, while adjusting the parameters until you have achieved good imaging. In our experience, once you find the optimal parameters you should be able to keep those same parameters across weeks.

 

== Tutorial on setting up a new wire-free Miniscope ==
=== 1) First we need to make sure we have all the components and software to get things up and running. ===
==== Major new Miniscope components that need to be ordered ====
The wire-free Miniscope uses all the same hardware and optics as the standard v3 Miniscope except for the focus slider and CMOS PCB. It also doesn't use the Miniscope DAQ PCB.
* '''Wire-free Miniscope Focus Slider''': You can get the wire-free focus slider machined by Shylo Stiteler <shylostiteler@gmail.com> or elsewhere. The design file and dimensions are in the "wire-free focus slider" folder in our github repository. When assembling the Miniscope, if the resistors on the PCB prevents the focus slider from fitting in snugly, you can use a scalpel to indent the top of the focus slider.
[[File:MS_FocusSlidervWireless.png|thumb|right|300px|Wire-free focus slider.]]
 
* '''Wire-free Miniscope CMOS PCB''': You will also need the wire-free CMOS PCB. '''''You can order this PCB already programmed and tested along with all the supporting equipment (batteries, connectors, chargers, SD Cards) from Filipe Carvalho <filipe@open-ephys.org>.''''' Of course you can also get this PCB made at your preferred PCB fab/assembly house as well. You can find the fabrication and assembly files in the "wire-free CMOS PCB" folder.
[[File:wire-free-PCB.png|thumb|right|300px|Wire-free PCB.]]
 

==== Additional components that may need to be ordered ====
The list below outlines the additional hardware and tools you need when setting up your own wire-free Miniscope. If you purchase a wire-free Miniscope system from Filipe Carvalho <filipe@open-ephys.org> you won't need the Atmel ICE as the PCB will already come programmed. Also, he can supply SDcards, batteries that are already wired up with the correct connectors, and an open-source lipo charging array with appropriate charge current.

If you are having the wire-free PCB produced somewhere else you will need the following:
* [https://www.digikey.com/products/en?mpart=ATATMEL-ICE&v=150 Atmel ICE] for programming the wire-free PCB
* Micro SD cards. We like to use [https://www.amazon.com/Sandisk-Extreme-MicroSDHC-UHS-I-SDSDQXL-032G-A46A/dp/B00G5R75AU/ref=sr_1_13?s=electronics&ie=UTF8&qid=1543963603&sr=1-13&keywords=sandisk+micro+sd+card+extreme these microSD cards]. The SanDisk microSD extreme cards seem to perform best.
* [https://www.powerstream.com/ultra-light.htm Small Lipo battery]. The 45mAH batteries seemed to work best and give us about 20 minutes of recording time. You may also want to purchase some batteries to test from wyon,https://www.wyon.ch/en/home.html. We are in the process of testing their W101 and W102 batteries. These might cut out another 0.5 grams if they work well.
* Mill-Max 50mil male and female headers. You can get these from digikey.com and they are used to connect the lipo battery and programmer to the CMOS PCB.
* [https://www.sparkfun.com/products/10217 Lipo battery charger]. Most single cell lipo chargers will work. You will need to modify many standard lipo chargers to limit their charging current to what your battery can handle. This is generally done by swapping on a surface mount resistor on the charger PCB.
* [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 50K Resistor]. ~50kOhm 0603 resistors to modify the battery charger.
* [https://www.amazon.com/Tekpower-TP3016M-Portable-Handheld-Variable/dp/B015OA1J82 Power source]. This could be helpful when we are programming and testing the PCB.
* [https://www.amazon.com/AmazonBasics-Male-Micro-Cable-Black/dp/B072J1BSV6/ref=sr_1_1_sspa?crid=19OWZCA50WRE7&keywords=micro+usb+amazon+basics&qid=1555957481&s=gateway&sprefix=micro+usb+amazon+%2Caps%2C337&sr=8-1-spons&psc=1 USB cable]. Micro USB cables to go with the lipo chargers.

==== Software to download ====

* Download [https://mh-nexus.de/en/hxd/ HxD]. This software will allow you to directly edit memory blocks of an SD card which will be needed to initially setup an SD card for wire-free Miniscope recording. '''NOTE''': This software will allow you to modify any byte of data on any drive connected to your computer so observe particular caution when using it.
* Download [https://www.microchip.com/mplab/avr-support/atmel-studio-7 Atmel Studio]. This will be used to program the microcontroller firmware onto the CMOS PCB.
* Download the wire-free Miniscope software found in the "wire-free Miniscope software" folder. This software will allow you to read and save wire-free Miniscope data from an SD card as well as allow you to program recording parameters (exposure, gain, recording length) to the SD card which the Miniscope will read.

=== 2) Now we need to get the wire-free CMOS PCB ready to be programmed with the wire-free Miniscope firmware. ===

==== Soldering the programming header ====
* First solder a 4 pin Mill-Max 50mil pitch header to the 4 pad programming interface on the wire-free CMOS PCB. The connections of this programming header are as follows:

[[File:wire-free-CMOS-PCB-Connections.png|thumb|right|600px|Programming header.]]
 

==== Soldering the lipo battery connector and excitation LED wires ====
* You can also now solder a 2 pin Mill-Max 50mil pitch header and wires for the excitation LED PCB to the three pads near to top of the board in the above picture. First solder the Mill-Max header to Lipo+ and GND (this will be the connector for the lipo battery). Then solder the 2 LED wires to LED+ and the same middle GND pad that the Mill-Max header is soldered to. The CMOS PCB should now look something like this:

[[File:Soldered-PCB-1.png|thumb|right|600px|PCB sensor side.]]

[[File:Soldered-PCB-2.png|thumb|right|600px|PCB sd card side.]]
 

==== Let's also connectorize the Lipo battery ====
* The lipo battery will come with 2 metal strips (initially protected with heat shrink) extending from the body of the battery which are its + and - voltage terminals. We want to solder a wire to each of these metal strips and then put a 2pin Mill-Max header on the other end of the wires so that the battery can connect to the Mill-Max header we soldered to the Lipo+ and GND pads of the CMOS PCB.
[[File:lipo-battery.png|thumb|right|600px|Lipo Battery.]]
 

* Make sure to never short the 2 metal strips of the lipo battery. If you do, it could damage the battery permanently.
* Use a multimeter to test which metal strip is the + and which is the - (GND).
* When soldering wires to the lipo, try to minimize the amount of heat traveling to the lipo battery.

=== 3) Programming the wire-free CMOS PCB ===
==== Connectorizing the Atmel ICE programmer ====
* In order to program the microcontroller on the CMOS PCB, we first need to wire-up and connectorize a 4pin Mill-Max header to the 4 programming pins of the Atmel ICE programmer. These are GND, VTG, SWDIO, and SWDCLK. Below shows which pins/wires of the Atmel ICE have which function. The Atmel ICE has 2 different 5x2 pin ports. One is labeled AVR and one is labeled SAM. Either will work but depending on which one you are using it will change which column you refer to in the below chart.

[[File:atmel-ice-swd-pinout.png|thumb|right|600px|Chart]]
 

* Connect the Atmel ICE to the programming header of the CMOS PCB.
* Power up the CMOS PCB through the lipo connector (2pin Mill-Max head with Lipo+ and GND). You can hook up a charged lipo battery but we suggest using a power supply between 3.5V and 4.2V here. This way you don't have to worry about a battery running out of charge during programming and testing. You can cap the maximum current output of the power source at 0.150A just to be safe. The power source should measure a current of about 0.03A when 3.8V is supplied to the PCB.
* When the CMOS PCB gets powered on, you should see an orange light turn on on the Atmel ICE which shows that the Atmel ICE has detected voltage on the VTG (Voltage Target) pin. In the ATATMEL-ICE-ND, you should see a red light turn on showing that the Atmel box is powered, and a green light showing that the box is measuring a voltage from the PCB. Updating Atmel Studio and restarting the computer could all help with debugging.
* Open Atmel Studio and click the "Device Programming" button

[[File:Atmel-device-programming.PNG|thumb|right|600px|Atmel Studio device programming button.]]
 

* In the Device Programming window that pops up select:
** Tool: Atmel ICE
** Device: ATSAM.... (should automatically be the correct name, ATSAME70N21)
** Interface: SWD
** Then click "Apply"
* Now check to make sure that Atmel Studio can communicate with the microcontroller on the CMOS PCB. You do this by clicking the "Read" button under Device Signature. If everything is powered and connected correctly you should see some numbers and letter pop up in the box and no error window show up. Now we are ready to program the microcontroller.

[[File:device-programming-window.PNG|thumb|right|600px|device programming window.]]
 

* Click "Memory" on the left menu panel of the Device Programming window we are currently in. If the memory tab is not showing up, make sure to select the tool, device, and interface and click apply again
* Click "Browse" and locate the wire-free Miniscope firmware. This is a .hex file you can find in the "/wire-free-firmware" folder. Either the .hex or .elf file should work.
* Click "Program". This will erase, program, and verify the microcontroller. It will tell you if everything was successful.
* Exit the Device Programming window.
* Now we have to do something a bit weird. I am not sure why this has to be done but it does. Open up the Atmel project found in the "/wire-free-firmware" folder. This load up the code that makes up the wire-free Miniscope firmware. Now click "Debug" from the top menu bar and then click "Start Debugging and Break". Wait about 15 seconds while the debugger does its thing in Atmel Studio and then the code should jump to the "main()" function and highlight it. Now click the play button (labelled "Start Debugging") in the top menu. Wait a few seconds then click the stop button (labelled "Stop Debugging").
[[File:loadingATMEL.PNG|thumb|right|600px|Loading Atmel.]]

[[File:ddebug-buttons.PNG|thumb|right|600px|Debug buttons.]]
 
* Go back to the "Device Programming" window by clicking the "Device Programming" button.
* Repeat the steps to program the PCB with the .hex file.
* Now the microcontroller on the wire-free Miniscope CMOS PCB knows how to be a wire-free Miniscope microcontroller.

=== 4) Configure the micro SD card ===
The wire-free Miniscope and the Miniscope SD Card Reader software are able to read and write raw data directly into and out of the memory blocks of the SD card. In memory block 1023 of the SD card, we need to first write an a key that will, for all subsequnt writing to the SD card, be checked before any raw data writed to make sure we are not writing to the wrong drive. '''If we accidently write over a memory block on your computer's drive it can corrupt Windows so we need to be extra careful not to do that.'''

==== Add the Write Key to memory block 1023 of the SD Card ====
Here we will use the HxD software to directly write our Key into the SD Card.
* Open the HxD software and run as Administrator
* Select 'Tools' then select 'Open Disk' from the drop down menu
* Uncheck the 'Open as Readonly' option in the bottom left of the window, select the SD card from the list of disks, and then click 'OK'. If the disk is not showing up, restarting the computer might help.

[[File:HxD1.PNG|thumb|right|600px|HxD.]]
 

* '''We will now be writing directly to memory blocks of the drive. Make sure you have selected the SD Card and not another drive'''
* Go to Sector 1023 and modify the first 16 bytes in this sector.We will be replacing the data in these 16 bytes with the write Key. The write Key is 0x0D7CBA17 repeated 4 times. After replacing these bytes it should look like this:
[[File:HxD2.PNG|thumb|right|600px|HxD write key.]]
 

* Now click 'Save'.
* Let's check to make sure everything was modified and saved correctly. Close HxD, pull out the SD card from the computer and then place it back in the computer. Now open up HxD, open the SD Card disk, go to sector 1023, and check to make sure the write Key is still there. If it is then we have correctly configured the SD Card for wire-free Miniscope recording.

=== 5) Using the Miniscope SD Card Reader software ===
Our final step is to use the Miniscope SD Card Reader software to configure the LED power and Gain of the wire-free Miniscope. The way we do this is by writing the configuration into specific bytes of memory block 1023 of the SD card. The Miniscope SD Card Reader software handles all of this through a simple GUI.
* Open the MiniscopeSDCardReader.exe and run as Administrator
[[File:MiniscopeSDCardReader.PNG|thumb|right|600px|Miniscope SD Card Reader.]]
 
* You may need to change the 'Drive' name based on the naming your computer has given to the SD Card. In the image above it has defaulted to 'PhysicalDrive1' and this name should usually work. If a window pops up asking if you want to format the SD card, do not format it or it will undo what we programmed.
* You can set the Gain, LED Power, and Recording Length. Once the correct numbers have been entered, click 'Set' to write those values to the SD card. The software makes sure the write Key is present in memory block 1023 before attempting to write this configuration. This is used to stop the software from writing to another disk but still be careful. A line should pop up in the bottom window saying “Write key match!”
* After setting the configuration you can take out the SD card from the computer and mount it in the wire-free Miniscope. Once the Miniscope is powered on, it will wait 5 seconds and then begin recording. Always put in the SD card before plugging in the battery.
* After recording with the Miniscope, take the SD card out of the Miniscope mount and place it in your computer. You can now use the MiniscopeSDCardReader software to view, save, and delete recordings.

=== 6) Modifying the Lipo charger ===
In general any single cell lipo charger will work for charging the batteries used for the wire-free Miniscope but you have to make sure that the max current the charge can output is limited to around 20mA. The Sparkfun Lipo charger listed at the top of this tutorial is capped at 500mA by default so we will need to modify the charger to limit the current to ~20mA. The way we do this is by replacing the SMD resistor circled in blue below with a ~50kOhm 0603 resistor. If you don't have a ~50kohn resistor on hand you can [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 order one from digikey]. If the solder around the resistor is hard to remove, it might help to add a little bit of new solder.

[[File:SparkfunChargerMod.png|thumb|right|600px|Sparkfun modified charger.]]
 

You will also need to modify or swap out the lipo connector on the right of the board with connector that can mate to the connector you put on your lipo batteries.

== How to record with the wire-free Miniscope system ==
After following the wire-free Miniscope tutorial above you should now be ready to record using the system. Imaging using the wire-free Miniscope has a few extra steps compared to the wired Miniscope but you set up a workflow for recording the system is often times easier to use than the wired one.

=== Steps for imaging in a unrestrained animal ===
# Use a wired Miniscope to get a ballpark idea of focal depth and excitation power needed for a specific animal.
# Set the focal height of the wire-free Miniscope as close as possible to the wired Miniscope you used in step 1.
# Using the MiniscopeSDCardReader software, set the Gain, LED Power, and recording length. We suggest using a ~5second recording length when first figuring out these settings. This will allow you to quickly image and then check the recording.
[[File:MiniscopeSDCardReader2.png|thumb|right|600px|Settings.]]
 
# Now that you have the focal depth set as well as the gain and LED power figured out, you are ready for your experiment. Mount the wire-free Miniscope on the baseplate on the animal's head.
# Place a microSD card in the SD card mount on the wire-free Miniscope PCB.
# Plug in a '''fully charged''' single cell lipo.
# The wire-free Miniscope will now power up and detect the SD card. You can also power up the Miniscope before mounting the SD card but we have found this to be slightly less stable than the other way around. '''The Miniscope will wait exactly 5 seconds''' before turning on its red status LED and beginning recording.
# The Miniscope will now record for the recording length you previously set through the MiniscopeSDCardReader software. Once the recording has finished the red status LED will turn off. Unplug the lipo battery then remove the SD card.
# Imaging data is stored in a raw format on the SD card. There are no files or folder structures on the SD card. The recording begins in memory block 1024 and will continue until the end of the recording is reached.

=== Steps for transferring a recording from an SD Card to a computer ===
Now that you have a wire-free Miniscope stored on an SD Card, we need to transfer it to a computer. As mentioned above, the wire-free Miniscope records raw pixel byte values directly to memory blocks in the SD Card. This means that when the card is mounted in a computer, the computer will think that the card needs to be reformatted. This is due to the SD Card not having a file system on it. '''Always ignore the recommendation of your computer to reformat the SD Card as well as if it says the SD Card is corrupted.'''
# Mount the SD Card in your computer. If you computer doesn't have a built in SD Card mount, you can use an external USB SD Card mount.
# Open the MiniscopeSDCardReader software in with Administrator privileges. You will need this since we will be directly reading/writing memory blocks.
## The "Drive" is the name of the SD Card. This defaults to "PhysicalDrive1" but you should double check you are using the correct name of the SD Card drive.
## The "Starting Sector" is the memory block where the beginning of the Miniscope recording is located. This should not need to ever be changed from "1024".
## '''Note''': Whenever this software attempts to access data on the SD Card, it first checks to make sure the correct 128bit "WRITE KEY" is stored in memory block 1023. This WRITE KEY was placed there by you if you followed the tutorial above. The goal of this WRITE KEY is it makes it extremely unlikely that you end up accessing or modifying any other drive on your computer since the chances of another drive having the 128bit WRITE KEY located at memory block 1023 is highly unlikely. When you do try accessing data on the SD Card, the text box at the bottom of the GUI will tell you if it found the correct WRITE KEY or if it found the wrong one and stopped the requested action.
# Now you can use the "Read/Save Data" portion of the software to do exactly that... read and/or save the wire-free Miniscope data.
## First enter in the length of the recording you want to extract from the SD Card. This says "Number of Seconds" but I think it is actually "Number of Frames" (''I will get around to fixing this sometime soon...''). The wire-free Miniscope records at 20FPS so you should usually just set this number a bit longer than the expected recording to make sure you grab all the data.
## If you click "Read" the software will open up a window that will play the wire-free Miniscope recording. On some computers using some versions of OpenCV, this option for some reason doesn't actually update the window and it just shows black the whole time. We recommend to use "Save" in all cases if this happens to you.
## If you click "Save" the software will display the video as it extracts it from the SD Card and writes it to the computer's drive. It will save a copy of the wire-free recording in the "data" folder located where ever your MiniscopeSDCardReader software is located. We generally recommend you using the "Save" option over the "Read" option since the read option can be buggy on some computers.
# Check to make sure the data is now saved as an uncompressed .avi file on your computer.
# Once you have your data transferred to your computer we highly recommend clearing the SD Card before beginning a new recording:
## You can do this using the "Clear SD Card" section of the software. Here you can define the number of frames to clear from the SD card and then clear/delete them.
## Set the number of frames to clear first. We suggest entering a number that is larger than the expected length of recording currently on the SD Card.
## Click "Delete" and the software will set all bytes in these memory block in the SD Card to 0.
## '''Note''': It will not delete the settings located in memory block 1023. This means you can now reuse this SD Card without reprogramming the gain, LED power, and recording length.
# '''Note''': Each frame is timestamped and the timestamp is embedded within each frame. You can extract the timestamp by generating a 32bit integer from the last 8th, 7th, 6th, and 5th pixels in each frame. In MATLAB it would look something like this for a given frame:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

You're Done!

Wire-free Miniscope

2019-05-21T02:27:20Z

Tristanshuman: /* Generally information, notes, and troubleshooting */

== Overview ==
The wire-free Miniscope is a battery powered, data logging Miniscope that is fully untethered from external DAQ and power hardware. This system is a modification to the current wired Miniscope system (version 3.2) and shares all the same components except for the focus slider, CMOS PCB, and DAQ PCB. Below covers everything needed to get up and running with the wire-free Miniscope system.

[[File:Wire-free.PNG|thumb|right|600px|Wire-free schematic and PCB.]]

=== Generally information, notes, and troubleshooting ===
* All design files, source code, firmware, and software can be found [https://github.com/Aharoni-Lab/Documentation-Internal/tree/master/Projects/Wire-Free-Miniscope here].
* The wire-free Miniscope's gain, excitation LED power, and recording length is configured on power-up once an microSD card is detected by the on board microcontroller. The microcontroller checks specific memory locations in the microSD card to load the configuration. Configurations are initially uploaded onto the microSD card using our MiniscopeSDCardReader software.
* Once the wire-free Miniscope has been powered up and a microSD card has been detected, the Miniscope waits 5 seconds then begins recording at 20FPS. At the start of recording the red status LED on the wire-free PCB will light up. Once recording has finished the red status LED will turn off. You can use the on and off timing of this LED to synchronize wire-free Minsicope recordings with an external behavioral camera.
* The last 12 pixels values of each frame recorded to the microSD card are over written with a footer that contains four 32bit values. The second to last 32bit value contains the time stamp of that frame. This timestamp is in milliseconds and relative to the start of recording. We have validated that this timestamp is extremely stable across 25 minute recordings. Below is an example code snippet of how you can reconstruct the timestamp for a give frame 'frame' in MATLAB:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

* The wire-free system will run on any single cell lipo battery (and more generally, with anything supplying between 4.2V and 3.4V that is capable of supplying ~80mA). With a 45mAh single cell lipo battery you can expect to get slightly over 20 minutes of recording.
* The suggested workflow is to first image the animals with a wired Miniscope to get an estimate of focal depth, gain, and excitation LED power. Set these parameters on the wire-free Miniscope and then do short recordings, checking the resulting video each time, while adjusting the parameters until you have achieved good imaging. In our experience, once you find the optimal parameters you should be able to keep those same parameters across weeks.

 

== Tutorial on setting up a new wire-free Miniscope ==
=== 1) First we need to make sure we have all the components and software to get things up and running. ===
==== Major new Miniscope components that need to be ordered ====
The wire-free Miniscope uses all the same hardware and optics as the standard v3 Miniscope except for the focus slider and CMOS PCB. It also doesn't use the Miniscope DAQ PCB.
* '''Wire-free Miniscope Focus Slider''': You can get the wire-free focus slider machined by Shylo Stiteler <shylostiteler@gmail.com> or elsewhere. The design file and dimensions are in the "wire-free focus slider" folder in our github repository. When assembling the Miniscope, if the resistors on the PCB prevents the focus slider from fitting in snugly, you can use a scalpel to indent the top of the focus slider.
[[File:MS_FocusSlidervWireless.png|thumb|right|300px|Wire-free focus slider.]]
 
* '''Wire-free Miniscope CMOS PCB''': You will also need the wire-free CMOS PCB. '''''You can order this PCB already programmed and tested along with all the supporting equipment (batteries, connectors, chargers, SD Cards) from Filipe Carvalho <filipe@open-ephys.org>.''''' Of course you can also get this PCB made at your preferred PCB fab/assembly house as well. You can find the fabrication and assembly files in the "wire-free CMOS PCB" folder.
[[File:wire-free-PCB.png|thumb|right|300px|Wire-free PCB.]]
 

==== Additional components that may need to be ordered ====
The list below outlines the additional hardware and tools you need when setting up your own wire-free Miniscope. If you purchase a wire-free Miniscope system from Filipe Carvalho <filipe@open-ephys.org> you won't need the Atmel ICE as the PCB will already come programmed. Also, he can supply SDcards, batteries that are already wired up with the correct connectors, and an open-source lipo charging array with appropriate charge current.

If you are having the wire-free PCB produced somewhere else you will need the following:
* [https://www.digikey.com/products/en?mpart=ATATMEL-ICE&v=150 Atmel ICE] for programming the wire-free PCB
* Micro SD cards. We like to use [https://www.amazon.com/Sandisk-Extreme-MicroSDHC-UHS-I-SDSDQXL-032G-A46A/dp/B00G5R75AU/ref=sr_1_13?s=electronics&ie=UTF8&qid=1543963603&sr=1-13&keywords=sandisk+micro+sd+card+extreme these microSD cards]. The SanDisk microSD extreme cards seem to perform best.
* [https://www.powerstream.com/ultra-light.htm Small Lipo battery]. The 45mAH batteries seemed to work best and give us about 20 minutes of recording time. You may also want to purchase some batteries to test from wyon,https://www.wyon.ch/en/home.html. We are in the process of testing their W101 and W102 batteries. These might cut out another 0.5 grams if they work well.
* Mill-Max 50mil male and female headers. You can get these from digikey.com and they are used to connect the lipo battery and programmer to the CMOS PCB.
* [https://www.sparkfun.com/products/10217 Lipo battery charger]. Most single cell lipo chargers will work. You will need to modify many standard lipo chargers to limit their charging current to what your battery can handle. This is generally done by swapping on a surface mount resistor on the charger PCB.
* [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 50K Resistor]. ~50kOhm 0603 resistors to modify the battery charger.
* [https://www.amazon.com/Tekpower-TP3016M-Portable-Handheld-Variable/dp/B015OA1J82 Power source]. This could be helpful when we are programming and testing the PCB.
* [https://www.amazon.com/AmazonBasics-Male-Micro-Cable-Black/dp/B072J1BSV6/ref=sr_1_1_sspa?crid=19OWZCA50WRE7&keywords=micro+usb+amazon+basics&qid=1555957481&s=gateway&sprefix=micro+usb+amazon+%2Caps%2C337&sr=8-1-spons&psc=1 USB cable]. Micro USB cables to go with the lipo chargers.

==== Software to download ====

* Download [https://mh-nexus.de/en/hxd/ HxD]. This software will allow you to directly edit memory blocks of an SD card which will be needed to initially setup an SD card for wire-free Miniscope recording. '''NOTE''': This software will allow you to modify any byte of data on any drive connected to your computer so observe particular caution when using it.
* Download [https://www.microchip.com/mplab/avr-support/atmel-studio-7 Atmel Studio]. This will be used to program the microcontroller firmware onto the CMOS PCB.
* Download the wire-free Miniscope software found in the "wire-free Miniscope software" folder. This software will allow you to read and save wire-free Miniscope data from an SD card as well as allow you to program recording parameters (exposure, gain, recording length) to the SD card which the Miniscope will read.

=== 2) Now we need to get the wire-free CMOS PCB ready to be programmed with the wire-free Miniscope firmware. ===

==== Soldering the programming header ====
* First solder a 4 pin Mill-Max 50mil pitch header to the 4 pad programming interface on the wire-free CMOS PCB. The connections of this programming header are as follows:

[[File:wire-free-CMOS-PCB-Connections.png|thumb|right|600px|Programming header.]]
 

==== Soldering the lipo battery connector and excitation LED wires ====
* You can also now solder a 2 pin Mill-Max 50mil pitch header and wires for the excitation LED PCB to the three pads near to top of the board in the above picture. First solder the Mill-Max header to Lipo+ and GND (this will be the connector for the lipo battery). Then solder the 2 LED wires to LED+ and the same middle GND pad that the Mill-Max header is soldered to. The CMOS PCB should now look something like this:

[[File:Soldered-PCB-1.png|thumb|right|600px|PCB sensor side.]]

[[File:Soldered-PCB-2.png|thumb|right|600px|PCB sd card side.]]
 

==== Let's also connectorize the Lipo battery ====
* The lipo battery will come with 2 metal strips (initially protected with heat shrink) extending from the body of the battery which are its + and - voltage terminals. We want to solder a wire to each of these metal strips and then put a 2pin Mill-Max header on the other end of the wires so that the battery can connect to the Mill-Max header we soldered to the Lipo+ and GND pads of the CMOS PCB.
[[File:lipo-battery.png|thumb|right|600px|Lipo Battery.]]
 

* Make sure to never short the 2 metal strips of the lipo battery. If you do, it could damage the battery permanently.
* Use a multimeter to test which metal strip is the + and which is the - (GND).
* When soldering wires to the lipo, try to minimize the amount of heat traveling to the lipo battery.

=== 3) Programming the wire-free CMOS PCB ===
==== Connectorizing the Atmel ICE programmer ====
* In order to program the microcontroller on the CMOS PCB, we first need to wire-up and connectorize a 4pin Mill-Max header to the 4 programming pins of the Atmel ICE programmer. These are GND, VTG, SWDIO, and SWDCLK. Below shows which pins/wires of the Atmel ICE have which function. The Atmel ICE has 2 different 5x2 pin ports. One is labeled AVR and one is labeled SAM. Either will work but depending on which one you are using it will change which column you refer to in the below chart.

[[File:atmel-ice-swd-pinout.png|thumb|right|600px|Chart]]
 

* Connect the Atmel ICE to the programming header of the CMOS PCB.
* Power up the CMOS PCB through the lipo connector (2pin Mill-Max head with Lipo+ and GND). You can hook up a charged lipo battery but we suggest using a power supply between 3.5V and 4.2V here. This way you don't have to worry about a battery running out of charge during programming and testing. You can cap the maximum current output of the power source at 0.150A just to be safe. The power source should measure a current of about 0.03A when 3.8V is supplied to the PCB.
* When the CMOS PCB gets powered on, you should see an orange light turn on on the Atmel ICE which shows that the Atmel ICE has detected voltage on the VTG (Voltage Target) pin. In the ATATMEL-ICE-ND, you should see a red light turn on showing that the Atmel box is powered, and a green light showing that the box is measuring a voltage from the PCB. Updating Atmel Studio and restarting the computer could all help with debugging.
* Open Atmel Studio and click the "Device Programming" button

[[File:Atmel-device-programming.PNG|thumb|right|600px|Atmel Studio device programming button.]]
 

* In the Device Programming window that pops up select:
** Tool: Atmel ICE
** Device: ATSAM.... (should automatically be the correct name, ATSAME70N21)
** Interface: SWD
** Then click "Apply"
* Now check to make sure that Atmel Studio can communicate with the microcontroller on the CMOS PCB. You do this by clicking the "Read" button under Device Signature. If everything is powered and connected correctly you should see some numbers and letter pop up in the box and no error window show up. Now we are ready to program the microcontroller.

[[File:device-programming-window.PNG|thumb|right|600px|device programming window.]]
 

* Click "Memory" on the left menu panel of the Device Programming window we are currently in. If the memory tab is not showing up, make sure to select the tool, device, and interface and click apply again
* Click "Browse" and locate the wire-free Miniscope firmware. This is a .hex file you can find in the "/wire-free-firmware" folder. Either the .hex or .elf file should work.
* Click "Program". This will erase, program, and verify the microcontroller. It will tell you if everything was successful.
* Exit the Device Programming window.
* Now we have to do something a bit weird. I am not sure why this has to be done but it does. Open up the Atmel project found in the "/wire-free-firmware" folder. This load up the code that makes up the wire-free Miniscope firmware. Now click "Debug" from the top menu bar and then click "Start Debugging and Break". Wait about 15 seconds while the debugger does its thing in Atmel Studio and then the code should jump to the "main()" function and highlight it. Now click the play button (labelled "Start Debugging") in the top menu. Wait a few seconds then click the stop button (labelled "Stop Debugging").
[[File:loadingATMEL.PNG|thumb|right|600px|Loading Atmel.]]

[[File:ddebug-buttons.PNG|thumb|right|600px|Debug buttons.]]
 
* Go back to the "Device Programming" window by clicking the "Device Programming" button.
* Repeat the steps to program the PCB with the .hex file.
* Now the microcontroller on the wire-free Miniscope CMOS PCB knows how to be a wire-free Miniscope microcontroller.

=== 4) Configure the micro SD card ===
The wire-free Miniscope and the Miniscope SD Card Reader software are able to read and write raw data directly into and out of the memory blocks of the SD card. In memory block 1023 of the SD card, we need to first write an a key that will, for all subsequnt writing to the SD card, be checked before any raw data writed to make sure we are not writing to the wrong drive. '''If we accidently write over a memory block on your computer's drive it can corrupt Windows so we need to be extra careful not to do that.'''

==== Add the Write Key to memory block 1023 of the SD Card ====
Here we will use the HxD software to directly write our Key into the SD Card.
* Open the HxD software and run as Administrator
* Select 'Tools' then select 'Open Disk' from the drop down menu
* Uncheck the 'Open as Readonly' option in the bottom left of the window, select the SD card from the list of disks, and then click 'OK'. If the disk is not showing up, restarting the computer might help.

[[File:HxD1.PNG|thumb|right|600px|HxD.]]
 

* '''We will now be writing directly to memory blocks of the drive. Make sure you have selected the SD Card and not another drive'''
* Go to Sector 1023 and modify the first 16 bytes in this sector.We will be replacing the data in these 16 bytes with the write Key. The write Key is 0x0D7CBA17 repeated 4 times. After replacing these bytes it should look like this:
[[File:HxD2.PNG|thumb|right|600px|HxD write key.]]
 

* Now click 'Save'.
* Let's check to make sure everything was modified and saved correctly. Close HxD, pull out the SD card from the computer and then place it back in the computer. Now open up HxD, open the SD Card disk, go to sector 1023, and check to make sure the write Key is still there. If it is then we have correctly configured the SD Card for wire-free Miniscope recording.

=== 5) Using the Miniscope SD Card Reader software ===
Our final step is to use the Miniscope SD Card Reader software to configure the LED power and Gain of the wire-free Miniscope. The way we do this is by writing the configuration into specific bytes of memory block 1023 of the SD card. The Miniscope SD Card Reader software handles all of this through a simple GUI.
* Open the MiniscopeSDCardReader.exe and run as Administrator
[[File:MiniscopeSDCardReader.PNG|thumb|right|600px|Miniscope SD Card Reader.]]
 
* You may need to change the 'Drive' name based on the naming your computer has given to the SD Card. In the image above it has defaulted to 'PhysicalDrive1' and this name should usually work. If a window pops up asking if you want to format the SD card, do not format it or it will undo what we programmed.
* You can set the Gain, LED Power, and Recording Length. Once the correct numbers have been entered, click 'Set' to write those values to the SD card. The software makes sure the write Key is present in memory block 1023 before attempting to write this configuration. This is used to stop the software from writing to another disk but still be careful. A line should pop up in the bottom window saying “Write key match!”
* After setting the configuration you can take out the SD card from the computer and mount it in the wire-free Miniscope. Once the Miniscope is powered on, it will wait 5 seconds and then begin recording. Always put in the SD card before plugging in the battery.
* After recording with the Miniscope, take the SD card out of the Miniscope mount and place it in your computer. You can now use the MiniscopeSDCardReader software to view, save, and delete recordings.

=== 6) Modifying the Lipo charger ===
In general any single cell lipo charger will work for charging the batteries used for the wire-free Miniscope but you have to make sure that the max current the charge can output is limited to around 20mA. The Sparkfun Lipo charger listed at the top of this tutorial is capped at 500mA by default so we will need to modify the charger to limit the current to ~20mA. The way we do this is by replacing the SMD resistor circled in blue below with a ~50kOhm 0603 resistor. If you don't have a ~50kohn resistor on hand you can [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 order one from digikey]. If the solder around the resistor is hard to remove, it might help to add a little bit of new solder.

[[File:SparkfunChargerMod.png|thumb|right|600px|Sparkfun modified charger.]]
 

You will also need to modify or swap out the lipo connector on the right of the board with connector that can mate to the connector you put on your lipo batteries.

== How to record with the wire-free Miniscope system ==
After following the wire-free Miniscope tutorial above you should now be ready to record using the system. Imaging using the wire-free Miniscope has a few extra steps compared to the wired Miniscope but you set up a workflow for recording the system is often times easier to use than the wired one.

=== Steps for imaging in a unrestrained animal ===
# Use a wired Miniscope to get a ballpark idea of focal depth and excitation power needed for a specific animal.
# Set the focal height of the wire-free Miniscope as close as possible to the wired Miniscope you used in step 1.
# Using the MiniscopeSDCardReader software, set the Gain, LED Power, and recording length. We suggest using a ~5second recording length when first figuring out these settings. This will allow you to quickly image and then check the recording.
[[File:MiniscopeSDCardReader2.png|thumb|right|600px|Settings.]]
 
# Now that you have the focal depth set as well as the gain and LED power figured out, you are ready for your experiment. Mount the wire-free Miniscope on the baseplate on the animal's head.
# Place a microSD card in the SD card mount on the wire-free Miniscope PCB.
# Plug in a '''fully charged''' single cell lipo.
# The wire-free Miniscope will now power up and detect the SD card. You can also power up the Miniscope before mounting the SD card but we have found this to be slightly less stable than the other way around. '''The Miniscope will wait exactly 5 seconds''' before turning on its red status LED and beginning recording.
# The Miniscope will now record for the recording length you previously set through the MiniscopeSDCardReader software. Once the recording has finished the red status LED will turn off. Unplug the lipo battery then remove the SD card.
# Imaging data is stored in a raw format on the SD card. There are no files or folder structures on the SD card. The recording begins in memory block 1024 and will continue until the end of the recording is reached.

=== Steps for transferring a recording from an SD Card to a computer ===
Now that you have a wire-free Miniscope stored on an SD Card, we need to transfer it to a computer. As mentioned above, the wire-free Miniscope records raw pixel byte values directly to memory blocks in the SD Card. This means that when the card is mounted in a computer, the computer will think that the card needs to be reformatted. This is due to the SD Card not having a file system on it. '''Always ignore the recommendation of your computer to reformat the SD Card as well as if it says the SD Card is corrupted.'''
# Mount the SD Card in your computer. If you computer doesn't have a built in SD Card mount, you can use an external USB SD Card mount.
# Open the MiniscopeSDCardReader software in with Administrator privileges. You will need this since we will be directly reading/writing memory blocks.
## The "Drive" is the name of the SD Card. This defaults to "PhysicalDrive1" but you should double check you are using the correct name of the SD Card drive.
## The "Starting Sector" is the memory block where the beginning of the Miniscope recording is located. This should not need to ever be changed from "1024".
## '''Note''': Whenever this software attempts to access data on the SD Card, it first checks to make sure the correct 128bit "WRITE KEY" is stored in memory block 1023. This WRITE KEY was placed there by you if you followed the tutorial above. The goal of this WRITE KEY is it makes it extremely unlikely that you end up accessing or modifying any other drive on your computer since the chances of another drive having the 128bit WRITE KEY located at memory block 1023 is highly unlikely. When you do try accessing data on the SD Card, the text box at the bottom of the GUI will tell you if it found the correct WRITE KEY or if it found the wrong one and stopped the requested action.
# Now you can use the "Read/Save Data" portion of the software to do exactly that... read and/or save the wire-free Miniscope data.
## First enter in the length of the recording you want to extract from the SD Card. This says "Number of Seconds" but I think it is actually "Number of Frames" (''I will get around to fixing this sometime soon...''). The wire-free Miniscope records at 20FPS so you should usually just set this number a bit longer than the expected recording to make sure you grab all the data.
## If you click "Read" the software will open up a window that will play the wire-free Miniscope recording. On some computers using some versions of OpenCV, this option for some reason doesn't actually update the window and it just shows black the whole time. We recommend to use "Save" in all cases if this happens to you.
## If you click "Save" the software will display the video as it extracts it from the SD Card and writes it to the computer's drive. It will save a copy of the wire-free recording in the "data" folder located where ever your MiniscopeSDCardReader software is located. We generally recommend you using the "Save" option over the "Read" option since the read option can be buggy on some computers.
# Check to make sure the data is now saved as an uncompressed .avi file on your computer.
# Once you have your data transferred to your computer we highly recommend clearing the SD Card before beginning a new recording:
## You can do this using the "Clear SD Card" section of the software. Here you can define the number of frames to clear from the SD card and then clear/delete them.
## Set the number of frames to clear first. We suggest entering a number that is larger than the expected length of recording currently on the SD Card.
## Click "Delete" and the software will set all bytes in these memory block in the SD Card to 0.
## '''Note''': It will not delete the settings located in memory block 1023. This means you can now reuse this SD Card without reprogramming the gain, LED power, and recording length.
# '''Note''': Each frame is timestamped and the timestamp is embedded within each frame. You can extract the timestamp by generating a 32bit integer from the last 8th, 7th, 6th, and 5th pixels in each frame. In MATLAB it would look something like this for a given frame:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

You're Done!

Wire-free Miniscope

2019-05-21T02:24:44Z

Tristanshuman: /* Generally information, notes, and troubleshooting */

== Overview ==
The wire-free Miniscope is a battery powered, data logging Miniscope that is fully untethered from external DAQ and power hardware. This system is a modification to the current wired Miniscope system (version 3.2) and shares all the same components except for the focus slider, CMOS PCB, and DAQ PCB. Below covers everything needed to get up and running with the wire-free Miniscope system.

[[File:Wire-free.PNG|thumb|right|600px|Wire-free schematic and PCB.]]

=== Generally information, notes, and troubleshooting ===
* All design files, source code, firmware, and software can be found [https://github.com/Aharoni-Lab/Documentation-Internal/tree/master/Projects/Wire-Free-Miniscope here].
* The wire-free Miniscope's gain, excitation LED power, and recording length is configured on power-up once an sdCard is detected by the on board microcontroller. The microcontroller checks specific memory locations in the sdCard to load the configuration. Configurations are initially uploaded onto the sdCard using our MiniscopeSDCardReader software.
* Once the wire-free Miniscope has been powered up and an sdCard has been detected, the Miniscope waits 5 seconds then begins recording at 20FPS. At the start of recording the red status LED on the wire-free PCB will light up. Once recording has finished the red status LED will turn off. You can use the on and off timing of this LED to synchronize wire-free Minsicope recordings with an external behavioral camera.
* The last 12 pixels values of each frame recorded to the sdCard are over written with a footer that contains four 32bit values. The second to last 32bit value contains the time stamp of that frame. This timestamp is in milliseconds and relative to the start of recording. We have validated that this timestamp is extremely stable across 25 minute recordings. Below is an example code snippet of how you can reconstruct the timestamp for a give frame 'frame' in MATLAB:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

* The wire-free system will run on any single cell lipo battery (and more generally, with anything supplying between 4.2V and 3.4V that is capable of supplying ~80mA). With a 45mAh single cell lipo battery you can expect to get slightly over 20 minutes of recording.
* The suggested workflow is to first image the animals with a wired Miniscope to get an estimate of focal depth, gain, and excitation LED power. Set these parameters on the wire-free Miniscope and then do short recordings, checking the resulting video each time, while adjusting the parameters until you have achieved good imaging. In our experience, once you find the optimal parameters you should be able to keep those same parameters across weeks.

 

== Tutorial on setting up a new wire-free Miniscope ==
=== 1) First we need to make sure we have all the components and software to get things up and running. ===
==== Major new Miniscope components that need to be ordered ====
The wire-free Miniscope uses all the same hardware and optics as the standard v3 Miniscope except for the focus slider and CMOS PCB. It also doesn't use the Miniscope DAQ PCB.
* '''Wire-free Miniscope Focus Slider''': You can get the wire-free focus slider machined by Shylo Stiteler <shylostiteler@gmail.com> or elsewhere. The design file and dimensions are in the "wire-free focus slider" folder in our github repository. When assembling the Miniscope, if the resistors on the PCB prevents the focus slider from fitting in snugly, you can use a scalpel to indent the top of the focus slider.
[[File:MS_FocusSlidervWireless.png|thumb|right|300px|Wire-free focus slider.]]
 
* '''Wire-free Miniscope CMOS PCB''': You will also need the wire-free CMOS PCB. '''''You can order this PCB already programmed and tested along with all the supporting equipment (batteries, connectors, chargers, SD Cards) from Filipe Carvalho <filipe@open-ephys.org>.''''' Of course you can also get this PCB made at your preferred PCB fab/assembly house as well. You can find the fabrication and assembly files in the "wire-free CMOS PCB" folder.
[[File:wire-free-PCB.png|thumb|right|300px|Wire-free PCB.]]
 

==== Additional components that may need to be ordered ====
The list below outlines the additional hardware and tools you need when setting up your own wire-free Miniscope. If you purchase a wire-free Miniscope system from Filipe Carvalho <filipe@open-ephys.org> you won't need the Atmel ICE as the PCB will already come programmed. Also, he can supply SDcards, batteries that are already wired up with the correct connectors, and an open-source lipo charging array with appropriate charge current.

If you are having the wire-free PCB produced somewhere else you will need the following:
* [https://www.digikey.com/products/en?mpart=ATATMEL-ICE&v=150 Atmel ICE] for programming the wire-free PCB
* Micro SD cards. We like to use [https://www.amazon.com/Sandisk-Extreme-MicroSDHC-UHS-I-SDSDQXL-032G-A46A/dp/B00G5R75AU/ref=sr_1_13?s=electronics&ie=UTF8&qid=1543963603&sr=1-13&keywords=sandisk+micro+sd+card+extreme these microSD cards]. The SanDisk microSD extreme cards seem to perform best.
* [https://www.powerstream.com/ultra-light.htm Small Lipo battery]. The 45mAH batteries seemed to work best and give us about 20 minutes of recording time. You may also want to purchase some batteries to test from wyon,https://www.wyon.ch/en/home.html. We are in the process of testing their W101 and W102 batteries. These might cut out another 0.5 grams if they work well.
* Mill-Max 50mil male and female headers. You can get these from digikey.com and they are used to connect the lipo battery and programmer to the CMOS PCB.
* [https://www.sparkfun.com/products/10217 Lipo battery charger]. Most single cell lipo chargers will work. You will need to modify many standard lipo chargers to limit their charging current to what your battery can handle. This is generally done by swapping on a surface mount resistor on the charger PCB.
* [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 50K Resistor]. ~50kOhm 0603 resistors to modify the battery charger.
* [https://www.amazon.com/Tekpower-TP3016M-Portable-Handheld-Variable/dp/B015OA1J82 Power source]. This could be helpful when we are programming and testing the PCB.
* [https://www.amazon.com/AmazonBasics-Male-Micro-Cable-Black/dp/B072J1BSV6/ref=sr_1_1_sspa?crid=19OWZCA50WRE7&keywords=micro+usb+amazon+basics&qid=1555957481&s=gateway&sprefix=micro+usb+amazon+%2Caps%2C337&sr=8-1-spons&psc=1 USB cable]. Micro USB cables to go with the lipo chargers.

==== Software to download ====

* Download [https://mh-nexus.de/en/hxd/ HxD]. This software will allow you to directly edit memory blocks of an SD card which will be needed to initially setup an SD card for wire-free Miniscope recording. '''NOTE''': This software will allow you to modify any byte of data on any drive connected to your computer so observe particular caution when using it.
* Download [https://www.microchip.com/mplab/avr-support/atmel-studio-7 Atmel Studio]. This will be used to program the microcontroller firmware onto the CMOS PCB.
* Download the wire-free Miniscope software found in the "wire-free Miniscope software" folder. This software will allow you to read and save wire-free Miniscope data from an SD card as well as allow you to program recording parameters (exposure, gain, recording length) to the SD card which the Miniscope will read.

=== 2) Now we need to get the wire-free CMOS PCB ready to be programmed with the wire-free Miniscope firmware. ===

==== Soldering the programming header ====
* First solder a 4 pin Mill-Max 50mil pitch header to the 4 pad programming interface on the wire-free CMOS PCB. The connections of this programming header are as follows:

[[File:wire-free-CMOS-PCB-Connections.png|thumb|right|600px|Programming header.]]
 

==== Soldering the lipo battery connector and excitation LED wires ====
* You can also now solder a 2 pin Mill-Max 50mil pitch header and wires for the excitation LED PCB to the three pads near to top of the board in the above picture. First solder the Mill-Max header to Lipo+ and GND (this will be the connector for the lipo battery). Then solder the 2 LED wires to LED+ and the same middle GND pad that the Mill-Max header is soldered to. The CMOS PCB should now look something like this:

[[File:Soldered-PCB-1.png|thumb|right|600px|PCB sensor side.]]

[[File:Soldered-PCB-2.png|thumb|right|600px|PCB sd card side.]]
 

==== Let's also connectorize the Lipo battery ====
* The lipo battery will come with 2 metal strips (initially protected with heat shrink) extending from the body of the battery which are its + and - voltage terminals. We want to solder a wire to each of these metal strips and then put a 2pin Mill-Max header on the other end of the wires so that the battery can connect to the Mill-Max header we soldered to the Lipo+ and GND pads of the CMOS PCB.
[[File:lipo-battery.png|thumb|right|600px|Lipo Battery.]]
 

* Make sure to never short the 2 metal strips of the lipo battery. If you do, it could damage the battery permanently.
* Use a multimeter to test which metal strip is the + and which is the - (GND).
* When soldering wires to the lipo, try to minimize the amount of heat traveling to the lipo battery.

=== 3) Programming the wire-free CMOS PCB ===
==== Connectorizing the Atmel ICE programmer ====
* In order to program the microcontroller on the CMOS PCB, we first need to wire-up and connectorize a 4pin Mill-Max header to the 4 programming pins of the Atmel ICE programmer. These are GND, VTG, SWDIO, and SWDCLK. Below shows which pins/wires of the Atmel ICE have which function. The Atmel ICE has 2 different 5x2 pin ports. One is labeled AVR and one is labeled SAM. Either will work but depending on which one you are using it will change which column you refer to in the below chart.

[[File:atmel-ice-swd-pinout.png|thumb|right|600px|Chart]]
 

* Connect the Atmel ICE to the programming header of the CMOS PCB.
* Power up the CMOS PCB through the lipo connector (2pin Mill-Max head with Lipo+ and GND). You can hook up a charged lipo battery but we suggest using a power supply between 3.5V and 4.2V here. This way you don't have to worry about a battery running out of charge during programming and testing. You can cap the maximum current output of the power source at 0.150A just to be safe. The power source should measure a current of about 0.03A when 3.8V is supplied to the PCB.
* When the CMOS PCB gets powered on, you should see an orange light turn on on the Atmel ICE which shows that the Atmel ICE has detected voltage on the VTG (Voltage Target) pin. In the ATATMEL-ICE-ND, you should see a red light turn on showing that the Atmel box is powered, and a green light showing that the box is measuring a voltage from the PCB. Updating Atmel Studio and restarting the computer could all help with debugging.
* Open Atmel Studio and click the "Device Programming" button

[[File:Atmel-device-programming.PNG|thumb|right|600px|Atmel Studio device programming button.]]
 

* In the Device Programming window that pops up select:
** Tool: Atmel ICE
** Device: ATSAM.... (should automatically be the correct name, ATSAME70N21)
** Interface: SWD
** Then click "Apply"
* Now check to make sure that Atmel Studio can communicate with the microcontroller on the CMOS PCB. You do this by clicking the "Read" button under Device Signature. If everything is powered and connected correctly you should see some numbers and letter pop up in the box and no error window show up. Now we are ready to program the microcontroller.

[[File:device-programming-window.PNG|thumb|right|600px|device programming window.]]
 

* Click "Memory" on the left menu panel of the Device Programming window we are currently in. If the memory tab is not showing up, make sure to select the tool, device, and interface and click apply again
* Click "Browse" and locate the wire-free Miniscope firmware. This is a .hex file you can find in the "/wire-free-firmware" folder. Either the .hex or .elf file should work.
* Click "Program". This will erase, program, and verify the microcontroller. It will tell you if everything was successful.
* Exit the Device Programming window.
* Now we have to do something a bit weird. I am not sure why this has to be done but it does. Open up the Atmel project found in the "/wire-free-firmware" folder. This load up the code that makes up the wire-free Miniscope firmware. Now click "Debug" from the top menu bar and then click "Start Debugging and Break". Wait about 15 seconds while the debugger does its thing in Atmel Studio and then the code should jump to the "main()" function and highlight it. Now click the play button (labelled "Start Debugging") in the top menu. Wait a few seconds then click the stop button (labelled "Stop Debugging").
[[File:loadingATMEL.PNG|thumb|right|600px|Loading Atmel.]]

[[File:ddebug-buttons.PNG|thumb|right|600px|Debug buttons.]]
 
* Go back to the "Device Programming" window by clicking the "Device Programming" button.
* Repeat the steps to program the PCB with the .hex file.
* Now the microcontroller on the wire-free Miniscope CMOS PCB knows how to be a wire-free Miniscope microcontroller.

=== 4) Configure the micro SD card ===
The wire-free Miniscope and the Miniscope SD Card Reader software are able to read and write raw data directly into and out of the memory blocks of the SD card. In memory block 1023 of the SD card, we need to first write an a key that will, for all subsequnt writing to the SD card, be checked before any raw data writed to make sure we are not writing to the wrong drive. '''If we accidently write over a memory block on your computer's drive it can corrupt Windows so we need to be extra careful not to do that.'''

==== Add the Write Key to memory block 1023 of the SD Card ====
Here we will use the HxD software to directly write our Key into the SD Card.
* Open the HxD software and run as Administrator
* Select 'Tools' then select 'Open Disk' from the drop down menu
* Uncheck the 'Open as Readonly' option in the bottom left of the window, select the SD card from the list of disks, and then click 'OK'. If the disk is not showing up, restarting the computer might help.

[[File:HxD1.PNG|thumb|right|600px|HxD.]]
 

* '''We will now be writing directly to memory blocks of the drive. Make sure you have selected the SD Card and not another drive'''
* Go to Sector 1023 and modify the first 16 bytes in this sector.We will be replacing the data in these 16 bytes with the write Key. The write Key is 0x0D7CBA17 repeated 4 times. After replacing these bytes it should look like this:
[[File:HxD2.PNG|thumb|right|600px|HxD write key.]]
 

* Now click 'Save'.
* Let's check to make sure everything was modified and saved correctly. Close HxD, pull out the SD card from the computer and then place it back in the computer. Now open up HxD, open the SD Card disk, go to sector 1023, and check to make sure the write Key is still there. If it is then we have correctly configured the SD Card for wire-free Miniscope recording.

=== 5) Using the Miniscope SD Card Reader software ===
Our final step is to use the Miniscope SD Card Reader software to configure the LED power and Gain of the wire-free Miniscope. The way we do this is by writing the configuration into specific bytes of memory block 1023 of the SD card. The Miniscope SD Card Reader software handles all of this through a simple GUI.
* Open the MiniscopeSDCardReader.exe and run as Administrator
[[File:MiniscopeSDCardReader.PNG|thumb|right|600px|Miniscope SD Card Reader.]]
 
* You may need to change the 'Drive' name based on the naming your computer has given to the SD Card. In the image above it has defaulted to 'PhysicalDrive1' and this name should usually work. If a window pops up asking if you want to format the SD card, do not format it or it will undo what we programmed.
* You can set the Gain, LED Power, and Recording Length. Once the correct numbers have been entered, click 'Set' to write those values to the SD card. The software makes sure the write Key is present in memory block 1023 before attempting to write this configuration. This is used to stop the software from writing to another disk but still be careful. A line should pop up in the bottom window saying “Write key match!”
* After setting the configuration you can take out the SD card from the computer and mount it in the wire-free Miniscope. Once the Miniscope is powered on, it will wait 5 seconds and then begin recording. Always put in the SD card before plugging in the battery.
* After recording with the Miniscope, take the SD card out of the Miniscope mount and place it in your computer. You can now use the MiniscopeSDCardReader software to view, save, and delete recordings.

=== 6) Modifying the Lipo charger ===
In general any single cell lipo charger will work for charging the batteries used for the wire-free Miniscope but you have to make sure that the max current the charge can output is limited to around 20mA. The Sparkfun Lipo charger listed at the top of this tutorial is capped at 500mA by default so we will need to modify the charger to limit the current to ~20mA. The way we do this is by replacing the SMD resistor circled in blue below with a ~50kOhm 0603 resistor. If you don't have a ~50kohn resistor on hand you can [https://www.digikey.com/product-detail/en/yageo/RC0603FR-0749K9L/311-49.9KHRCT-ND/730212 order one from digikey]. If the solder around the resistor is hard to remove, it might help to add a little bit of new solder.

[[File:SparkfunChargerMod.png|thumb|right|600px|Sparkfun modified charger.]]
 

You will also need to modify or swap out the lipo connector on the right of the board with connector that can mate to the connector you put on your lipo batteries.

== How to record with the wire-free Miniscope system ==
After following the wire-free Miniscope tutorial above you should now be ready to record using the system. Imaging using the wire-free Miniscope has a few extra steps compared to the wired Miniscope but you set up a workflow for recording the system is often times easier to use than the wired one.

=== Steps for imaging in a unrestrained animal ===
# Use a wired Miniscope to get a ballpark idea of focal depth and excitation power needed for a specific animal.
# Set the focal height of the wire-free Miniscope as close as possible to the wired Miniscope you used in step 1.
# Using the MiniscopeSDCardReader software, set the Gain, LED Power, and recording length. We suggest using a ~5second recording length when first figuring out these settings. This will allow you to quickly image and then check the recording.
[[File:MiniscopeSDCardReader2.png|thumb|right|600px|Settings.]]
 
# Now that you have the focal depth set as well as the gain and LED power figured out, you are ready for your experiment. Mount the wire-free Miniscope on the baseplate on the animal's head.
# Place a microSD card in the SD card mount on the wire-free Miniscope PCB.
# Plug in a '''fully charged''' single cell lipo.
# The wire-free Miniscope will now power up and detect the SD card. You can also power up the Miniscope before mounting the SD card but we have found this to be slightly less stable than the other way around. '''The Miniscope will wait exactly 5 seconds''' before turning on its red status LED and beginning recording.
# The Miniscope will now record for the recording length you previously set through the MiniscopeSDCardReader software. Once the recording has finished the red status LED will turn off. Unplug the lipo battery then remove the SD card.
# Imaging data is stored in a raw format on the SD card. There are no files or folder structures on the SD card. The recording begins in memory block 1024 and will continue until the end of the recording is reached.

=== Steps for transferring a recording from an SD Card to a computer ===
Now that you have a wire-free Miniscope stored on an SD Card, we need to transfer it to a computer. As mentioned above, the wire-free Miniscope records raw pixel byte values directly to memory blocks in the SD Card. This means that when the card is mounted in a computer, the computer will think that the card needs to be reformatted. This is due to the SD Card not having a file system on it. '''Always ignore the recommendation of your computer to reformat the SD Card as well as if it says the SD Card is corrupted.'''
# Mount the SD Card in your computer. If you computer doesn't have a built in SD Card mount, you can use an external USB SD Card mount.
# Open the MiniscopeSDCardReader software in with Administrator privileges. You will need this since we will be directly reading/writing memory blocks.
## The "Drive" is the name of the SD Card. This defaults to "PhysicalDrive1" but you should double check you are using the correct name of the SD Card drive.
## The "Starting Sector" is the memory block where the beginning of the Miniscope recording is located. This should not need to ever be changed from "1024".
## '''Note''': Whenever this software attempts to access data on the SD Card, it first checks to make sure the correct 128bit "WRITE KEY" is stored in memory block 1023. This WRITE KEY was placed there by you if you followed the tutorial above. The goal of this WRITE KEY is it makes it extremely unlikely that you end up accessing or modifying any other drive on your computer since the chances of another drive having the 128bit WRITE KEY located at memory block 1023 is highly unlikely. When you do try accessing data on the SD Card, the text box at the bottom of the GUI will tell you if it found the correct WRITE KEY or if it found the wrong one and stopped the requested action.
# Now you can use the "Read/Save Data" portion of the software to do exactly that... read and/or save the wire-free Miniscope data.
## First enter in the length of the recording you want to extract from the SD Card. This says "Number of Seconds" but I think it is actually "Number of Frames" (''I will get around to fixing this sometime soon...''). The wire-free Miniscope records at 20FPS so you should usually just set this number a bit longer than the expected recording to make sure you grab all the data.
## If you click "Read" the software will open up a window that will play the wire-free Miniscope recording. On some computers using some versions of OpenCV, this option for some reason doesn't actually update the window and it just shows black the whole time. We recommend to use "Save" in all cases if this happens to you.
## If you click "Save" the software will display the video as it extracts it from the SD Card and writes it to the computer's drive. It will save a copy of the wire-free recording in the "data" folder located where ever your MiniscopeSDCardReader software is located. We generally recommend you using the "Save" option over the "Read" option since the read option can be buggy on some computers.
# Check to make sure the data is now saved as an uncompressed .avi file on your computer.
# Once you have your data transferred to your computer we highly recommend clearing the SD Card before beginning a new recording:
## You can do this using the "Clear SD Card" section of the software. Here you can define the number of frames to clear from the SD card and then clear/delete them.
## Set the number of frames to clear first. We suggest entering a number that is larger than the expected length of recording currently on the SD Card.
## Click "Delete" and the software will set all bytes in these memory block in the SD Card to 0.
## '''Note''': It will not delete the settings located in memory block 1023. This means you can now reuse this SD Card without reprogramming the gain, LED power, and recording length.
# '''Note''': Each frame is timestamped and the timestamp is embedded within each frame. You can extract the timestamp by generating a 32bit integer from the last 8th, 7th, 6th, and 5th pixels in each frame. In MATLAB it would look something like this for a given frame:

<code>footer = (frame(end,(end-7):end)); timestamp = footer(1) + bitshift(footer(2),8) + bitshift(footer(3),16) + bitshift(footer(4),24); </code>

You're Done!

Online Workshop

2018-05-14T21:29:56Z

Tristanshuman: /* Surgery Procedure and Baseplating */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://drive.google.com/open?id=0B1RSzZP5s3hhQ2RKQXpBcThVUVk Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/open?id=1_slc0IJLrswAmw_4z1oXQnhDRDnEQmcB Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://ucla.box.com/s/qd4aikyy1tk3iciqgfx73urr6dcc45mv Sample Imaging Data]

[https://drive.google.com/open?id=0B1RSzZP5s3hhcFVhRm9QVW5fUHM Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[[Initial Testing of Assembled Miniscopes]]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Online Workshop

2018-05-14T21:29:26Z

Tristanshuman: /* Surgery Procedure and Baseplating */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://drive.google.com/open?id=0B1RSzZP5s3hhQ2RKQXpBcThVUVk Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/open?id=1_slc0IJLrswAmw_4z1oXQnhDRDnEQmcB | Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://ucla.box.com/s/qd4aikyy1tk3iciqgfx73urr6dcc45mv Sample Imaging Data]

[https://drive.google.com/open?id=0B1RSzZP5s3hhcFVhRm9QVW5fUHM Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[[Initial Testing of Assembled Miniscopes]]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Online Workshop

2017-10-13T14:55:06Z

Tristanshuman: /* Surgery Procedure and Baseplating */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://drive.google.com/open?id=0B1RSzZP5s3hhQ2RKQXpBcThVUVk Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/a/g.ucla.edu/file/d/0B-x_dM_VK0wKREFRMFR0Ri1rdnM/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://drive.google.com/open?id=0B1RSzZP5s3hhcFVhRm9QVW5fUHM Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[[Initial Testing of Assembled Miniscopes]]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Online Workshop

2017-10-13T14:54:55Z

Tristanshuman: /* Surgery Procedure and Baseplating */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://drive.google.com/open?id=0B1RSzZP5s3hhQ2RKQXpBcThVUVk Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/a/g.ucla.edu/file/d/0B-x_dM_VK0wKREFRMFR0Ri1rdnM/view?usp=sharing | Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://drive.google.com/open?id=0B1RSzZP5s3hhcFVhRm9QVW5fUHM Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[[Initial Testing of Assembled Miniscopes]]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

User:Tristanshuman

2017-09-05T19:21:00Z

Tristanshuman:

Tristan Shuman, PhD 
Assistant Professor 
Department of Neuroscience 
Icahn School of Medicine at Mount Sinai 
tristan.shuman@mssm.edu

My lab uses in vivo calcium imaging and electrophysiology to study the neural circuits that produce behavior and how these circuits are altered in models of disease such as epilepsy and autism.

http://labs.neuroscience.mssm.edu/project/shuman-lab/

Contributors

2017-09-05T14:36:20Z

Tristanshuman:

This project began as a collaboration between the Golshani Lab, Silva Lab, and Khakh Lab at the University of California, Los Angeles.

;Peyman Golshani
:Associate Professor, Department of Neurology at David Geffen School of Medicine, UCLA
:pgolshani@mednet.ucla.edu

;Alcino Silva
:Professor, Neurobiology, Psychiatry and Psychology, UCLA
:Silvaa@mednet.ucla.edu

;Baljit Khakh
:Professor, Physiology and Neurobiology, UCLA
:bkhakh@mednet.ucla.edu

;Daniel Aharoni
:Adjunct Assistant Professor, UCLA
:DAharoni@mednet.ucla.edu

;Tristan Shuman
:Assistant Professor, Icahn School of Medicine at Mount Sinai
:tristan.shuman@mssm.edu

;Denise Cai
:Assistant Professor, Icahn School of Medicine at Mount Sinai
:denise.cai@mssm.edu

;Christopher Lee
:Research Associate, Shuman Lab, Icahn School of Medicine at Mount Sinai
:christopher.lee1@mssm.edu

;Katie Maguire
:Lab Manager, Golshani Lab, UCLA
:k8t.maguire@gmail.com

Contributors

2017-09-05T14:34:51Z

Tristanshuman:

This project began as a collaboration between the Golshani Lab, Silva Lab, and Khakh Lab at the University of California, Los Angeles.

;Peyman Golshani
:Department of Neurology at David Geffen School of Medicine, UCLA
:pgolshani@mednet.ucla.edu

;Alcino Silva
:Neurobiology, Psychiatry and Psychology, UCLA
:Silvaa@mednet.ucla.edu

;Baljit Khakh
:Physiology and Neurobiology, UCLA
:bkhakh@mednet.ucla.edu

;Daniel Aharoni
:Adjunct Assistant Professor, UCLA
:DAharoni@mednet.ucla.edu

;Tristan Shuman
:Assistant Professor, Icahn School of Medicine at Mount Sinai
:tristan.shuman@mssm.edu

;Denise Cai
:Assistant Professor, Icahn School of Medicine at Mount Sinai
:denise.cai@mssm.edu

;Christopher Lee
:Research Associate, Shuman Lab, Icahn School of Medicine at Mount Sinai
:christopher.lee1@mssm.edu

;Katie Maguire
:Lab Manager, Golshani Lab, UCLA
:k8t.maguire@gmail.com

Contributors

2017-09-05T14:33:16Z

Tristanshuman:

This project began as a collaboration between the Golshani Lab, Silva Lab, and Khakh Lab at the University of California, Los Angeles.

;Peyman Golshani
:Department of Neurology at David Geffen School of Medicine, UCLA


;Alcino Silva
:Neurobiology, Psychiatry and Psychology, UCLA


;Baljit Khakh
:Physiology and Neurobiology, UCLA


;Daniel Aharoni
:Adjunct Assistant Professor, UCLA
:DAharoni@mednet.ucla.edu

;Tristan Shuman
:Assistant Professor, Icahn School of Medicine at Mount Sinai
:tristan.shuman@mssm.edu

;Denise Cai
:Assistant Professor, Icahn School of Medicine at Mount Sinai
:denise.cai@mssm.edu

;Christopher Lee
:Research Associate, Shuman Lab, Icahn School of Medicine at Mount Sinai

;Katie Maguire
:Lab Manager, Golshani Lab, UCLA

Part Procurement

2017-09-05T14:06:59Z

Tristanshuman:

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===

Note: You can sign up for the group order on [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to purchase CMOS PCBs and DAQ PCBs at reduced cost.

'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' folder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [http://www.custompcb.com/ Silver Circuits]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===

Note: You can sign up for the group order on [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to purchase CMOS PCBs and DAQ PCBs at reduced cost.

Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T14:05:06Z

Tristanshuman: /* Data Acquisition PCB */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===

Note: You can sign up for the group order on [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to purchase CMOS PCBs and DAQ PCBs at reduced cost.

'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' folder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [http://www.custompcb.com/ Silver Circuits]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===

Note: You can sign up for the group order on [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to purchase CMOS PCBs and DAQ PCBs at reduced cost.

Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T14:04:48Z

Tristanshuman: /* CMOS Imaging Sensor PCB */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===

Note: You can sign up for the group order on [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to purchase CMOS PCBs and DAQ PCBs at reduced cost.

'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' folder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [http://www.custompcb.com/ Silver Circuits]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T14:03:53Z

Tristanshuman: /* CMOS Imaging Sensor PCB */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===

Note: You can sign up for the group order on [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet].

'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' folder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [http://www.custompcb.com/ Silver Circuits]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T14:00:17Z

Tristanshuman: /* Excitation LED PCB */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===
'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' folder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [http://www.custompcb.com/ Silver Circuits]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T13:58:51Z

Tristanshuman: /* CMOS Imaging Sensor PCB */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===
'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' folder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [[http://www.custompcb.com/ Silver Circuits]]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T13:55:44Z

Tristanshuman: /* General Note on PCB Fabrication and Assembly */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to [https://docs.google.com/spreadsheets/d/14wKD1-nZVGhdf2VnJYl1scEssredgB64XKHe5C0PY0k/edit#gid=0 this signup sheet] to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===
'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [[http://www.custompcb.com/ Silver Circuits]]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T13:55:11Z

Tristanshuman: /* General Note on PCB Fabrication and Assembly */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [http://miniscope.org/board/ Discussion Board] for those labs to get in touch with each other. You can also go directly to this signup sheet to put your name on the wait list.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===
'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [[http://www.custompcb.com/ Silver Circuits]]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Part Procurement

2017-09-05T13:49:12Z

Tristanshuman: /* General Note on PCB Fabrication and Assembly */

The miniscope system is consists of a machined plastic housing, custom Printed Circuit Boards (PCBs), and off the shelf components. This guide will take you through the process of ordering everything you need to build a system of your own.

== General Note on PCB Fabrication and Assembly ==
Pricing for small batch PCB fabrication and assembly is usually dominated by the one time cost of the PCB manufacturer setting up their equipment for the specific order. When ordering 1000's of PCBs this cost is negligible but for orders of 1 to 10 PCBs this cost effectively greatly increases the per board cost.

We have been contacted by a many labs interested in coordinating larger orders of PCBs to decrease the per board price and have set up a thread on the [[Discussion Board]] for those labs to get in touch with each other.

'''For our own labs we usually aim for the following quantities when ordering:'''
;DAQ PCB:
:Fabrication: 20 PCBs. The '''total price''' for fabrication will likely be the same for quantities of 20 or less of this board so you might as well order the maximum number of boards.
:Assembly: 10 PCBs. Assembly is less affected by the one time setup fee so smaller quantities will have a less dramatic per board price change when increasing total quantity. We aim for getting at least 10 PCBs assembled at a time but the cost for doing just 2-4 is still pretty reasonable.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/a/ad/DAQ_PCB_Quote_Sierra_Circuits.pdf DAQ PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you. The other option would be to order the components yourself and ship them to Sierra Circuits.
;CMOS Imaging Sensor PCB:
:Fabrication: 50 to 100 PCBs. Again, the '''total price''' will likely stay the same for quantities under 50 to 100 of these boards.
:Assembly: 10 PCBs. Just like with the DAQ PCB, per board assembly cost will change less dramatically with smaller quantity orders.
:Price quote you can reference from Sierra Circuits: [http://miniscope.org/images/8/89/CMOS_Imaging_Sensor_PCB_Quote_Sierra_Circuits.pdf CMOS Imaging Sensor PCB Quote]. The quote for 'Components' is for Sierra Circuits to order all the electrical components for you ('''except the CMOS imaging sensor which you can ask to see if they can source as well'''). Please make reference to '''version 3.2''' of the CMOS Imaging sensor PCB when talking with Sierra Circuits and it could be helpful to link to our [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB/tree/master/v3_2 GitHub repository].The other option would be to order the components yourself and ship them to Sierra Circuits.
;Excitation LED PCB
:This board only requires basic fabrication technology which doesn't have a high one time setup fee. We suggest using Silver Circuits PCB Fabricators for this board.

== Miniscope Master Parts List ==
An up-to-date list of all components (besides electrical components listed in the each PCB project's Bill of Materials (BoM)) can be found in our Google Documents [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list]. All components on this list should have less than a two week lead time except
*GRIN lenses (see [[GRIN Lens Information]])
*CMOS Imaging Sensor
After running through the procurement details below make sure to double check with the parts list that all components have been ordered.
== Head Mounted Scope ==
=== Machined Housing Parts ===
The design files for all parts that need to be machined can be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. We have included both the Solidworks files as well as exported each part as a .stl.

The three housing components (MainBody, FocusingSlider, FilterSetCover) are CNC machined out of Delrin plastic. While the parts themselves are not too complex, their small size and thin walls makes them tricky to machine. Your campus machine shop should be able to machine these parts for you but generally this will take longer and be significantly more expensive than sending the parts out for machining.

Shylo Stiteler is a local machinist that is very familiar with our project. You can contact Shylo by email, shylostiteler@gmail.com, with the parts you need machined. His work is very reasonably priced, quick, and consistent.

We also should mention [https://www.protolabs.com/ Protolabs] for general machining projects. They are very quick and reliable but will not machine parts with wall thickness under 1mm. This means they won't be able to machine the majority of scope parts without added addition mass.

=== Machined Aluminum Baseplate ===
The design file for the Baseplate can also be found on the [https://github.com/daharoni/Miniscope_Machined_Parts.git Miniscope Machined Parts Github Repository]. Similar to what is stated above, this part can likely be machined by your local machine shop but we recommend getting the part machined by Shylo Stiteler's company, shylostiteler@gmail.com.

=== Optical Components ===
The optical components in the microscope are all off the shelf components which generally have less than a week lead time to arrive.
;Diced filter set
:We use Chroma filters sets in all our scopes but have also had success with Semrock and Omega Optical filters. All three of these companies will dice their standard filters to what ever size you need. The filter set and dice dimensions we use can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list], and you can contact Dick Stewart <dstewart@chroma.com> for a price quote.
;Internal lenses
:Both the half-ball lens and achromatic lens can be purchased through [http://www.edmundoptics.com/ Edmund Optics]. Part numbers can be found on our [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].
;GRIN lenses
:Acquiring GRIN lenses may prove a bit more complicated than acquiring the rest of the components in our system. For this reason we have a [[GRIN Lens Information|dedicated GRIN lens page]] on this topic.

=== CMOS Imaging Sensor PCB ===
'''IMPORTANT''': If you downloaded the CMOS Imaging Sensor PCB files before January 27, 2015 please update them with the current version on GitHub.

Design, fabrication, and assembly files can be found that the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB.git Miniscope CMOS imaging sensor PCB Github repository]. The newest version of the PCB can be found in folder 'v3_2'.

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.031" thick FR4 circuit board with In Pad Vias.
*'CMOS_v3_2_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components.
*'Serializer_System2_MT9V032_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'CMOS_v3_2_Assy_Info.docx' has all the relevant information for PCB assembly.

While it is possible to assemble this PCB yourself, we suggest most labs send it out to a professional assembly house. For both fabrication and assembly we recommend using [https://www.protoexpress.com/ Sierra Circuits]. The gerber files and board information document are needed for fabrication. The BOM (Bill of Materials) file and PnP (Pick and Place) file are needed for assembly. Generally PCB assembly houses can provide turnkey services which means they will not only assembly the PCB but also handle ordering all the individual components for a small markup.

In order to minimize the size of this PCB, buried vias and two sided assembly are used which results in a higher production costs than more standard boards. When getting a price quote we suggest asking for pricing at a few different quantities (5, 10, 20 boards). At these small quantities there is usually a range of quantities where the overall price remains practically the same for fabricating and assembly more boards.

:''' IMPORTANT: Ordering the Imaging Sensor:''' All electrical components can be easily purchased through Digikey except for the imaging sensor. You should order the imaging sensor yourself and send it in to be assembled ('''Note:''' Currently Sierra Circuits should be able to source the imaging sensor as well so ask when requesting a quote). The CMOS imaging sensor used is the Aptina (or OnSemiconductor) MT9V032C12STM and can be found through Arrow Electronics or Aliexpress.

=== Excitation LED PCB ===
Design and fabrication files can be found at the [https://github.com/daharoni/Miniscope_Excitation_LED_PCB.git Miniscope Excitation LED PCB GitHub Repository].

The technology needed to fabrication this board is much simpler than what is needed for the CMOS imaging sensor PCB and DAQ PCB. For this reason we suggest using the 'PCB Production' option through [[http://www.custompcb.com/ Silver Circuits]]. You can upload the gerber files directly to their site for a price quote but we suggest emailing them to get a better deal.

If you want to get the standard Excitation LED PCBs made you can just email sales@custompcb.com and tell them that you would like to purchase Order # 7500 (no need to include any design/fabrication files). This will give you 125 PCB for a little over $200. While 125 PCBs (the minimum order) is more than what is needed for most labs, the total price will still be significantly cheaper than most other PCB fabrication companies.

'''Fabrication Properties:'''
*Number of layers: 2
*Substrate: 0.031” FR4
*Board width: 5mm
*Board height: 7.5mm
*Copper weight: 1oz (not important)
*Surface: HASL or ENIG (not important)
*Board shape: Custom
*Cutouts: None
*Solder mask color: Black
*Sinkscreen layers: Bottom
*Sinkscreen color: White
*Electrical Test: Not required
*Routing: Either individual or panalized with v-scores
*Ask to get them panelized on 4"x5" PCBs

=== Miscellaneous Parts ===

== Data Acquisition System ==
The DAQ system is composed of a DAQ PCB and 3D printed housing. The DAQ PCB needs to be fabricated and assembled by a PCB Fab and Assembly House capable of handling prototype and low volume orders (we suggest Sierra Circuits). In general you will mainly be paying for the setup cost when getting low volumes of PCBs fabricated and assembled. For this reason it is cost effective to ask for a price quote at multiple quantities (1, 5, 10, 20) to get an idea of price breakdown. For these DAQ PCBs it will cost around the same amount to get 1, 5, 10 produced.

=== Data Acquisition PCB ===
Design, fabrication, and assembly files can be found at the [https://github.com/daharoni/Miniscope_DAQ_PCB.git Miniscope DAQ PCB Github repository].

The 'Fabrication Files' folder contains all the information needed to get the PCB fabricated. PCB fabrication means the PCB is printed but not assembled. The PCB is a 4 layer, 0.062" thick FR4 circuit board with controlled impedance and tented vias. The DAQ board contains a 0.8mm pitch BGA component so the surface finish needs to be ENIG.
*'Miniscope_DAQ_PCB_Fab_Info.docx' has all the relevant specs for PCB fabrication.

The 'Assembly Files' filder contains all the information needed to get the fabricated circuit board assembled with electrical components. I usually have all components except the through-hole components assembly by an Assembly House but you can have the through-hole components assembled by them as well. You will need to modify the Bill of Materials (BOM) depending on which components you want assembled.
*'USB_Control_FPD_Linkv2_BOM.xlsx' lists all electrical components needed for assembly along with each components PCB designator. A PCB assembly house can likely offer a turn-key assembly solution where they will hand the ordering of all these components for a small markup. You can also order them yourself and ship them as a kit to the assembler.
*'Miniscope_DAQ_PCB_Assy_Info.docx' has all the relevant information for PCB assembly.

=== DAQ PCB Case ===
We have designed a simple case to enclose and protect the DAQ PCB which can be 3D printed [https://www.shapeways.com/product/W36FP33SB/daq-box-fpd-linkv3-2?key=87d91ef60375b2e47acf68ae23f7cb08 here] for v3.2 and [https://www.shapeways.com/product/68GH35EES/daq-box-fpd-link?key=22e8501f96c41efb1a85b1b04b40d32b here] for v3.1.

=== Miscellaneous Parts ===

== Cabling and Connector==
On the 'Head Mounted Scope' page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] you will find part numbers for 2 coaxial cable options as well as the suggested SMA coaxial connector. Even if you are experienced with soldering, we suggest using the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB Coax2SMA PCB] along with an edge mounted SMA connector to connectorize the coax cables. The Coax2SMA PCB is a very simple PCB that any PCB fabrication house can produce. We suggest using the link below to have these PCBs fabricated by OSH Park (very quick, cheap, and easy).

[https://oshpark.com/shared_projects/xtQGQ32E Order from OSH Park]

== Tools ==
There is a dedicated page of the [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list] outlining the tools you will need for assembly of the Miniscope system.

Main Page

2017-09-05T13:39:00Z

Tristanshuman: /* Current Status of Project */

[[File:miniscopev2.JPG|thumb|300px]]
'''Welcome to Miniscope.org Wiki! Follow the project on Twitter: [https://twitter.com/MiniscopeTeam @MiniscopeTeam].'''

The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Stanford and published in a [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1694.html paper in Nature Methods in 2011]. It uses wide-field fluorescence imaging to record neural activity in awake, freely moving mice. The microscope introduced here (Miniscope) has a mass of 3 grams and uses a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data to custom open source Data Acquisition (DAQ) hardware and software. This wiki site provides a centralized location for sharing design files, source code, and other relevant information so that a community of users can share ideas and developments related to this important imaging technique. Our goal is to help disseminate this technology to the larger neuroscience community and build a foundation of users that will continue advancing this technology and contribute back to the project. While the Miniscope system described here is not an off-the-shelf commercial solution, we have focused on making it as easy as possible for the average neuroscience lab to build and modify, requiring minimal soldering and hands on assembly. For more information please visit the [[Overview of System Components|Project Overview]] page. The Miniscope project and Miniscope.org are still works in progress and will be routinely updated over the coming months and years. We hope you will contribute to this important process!

== Current Status of Project ==
The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. Miniscopes were used to understand how the brain links memories across time, with the findings published in [http://www.nature.com/nature/journal/v534/n7605/full/nature17955.html Nature, 2016]. The work and files available on this site are the most up-to-date public version of our system and will be updated frequently with improvements and new system features. Again, we hope that you will contribute to this development process! This wiki is designed for this very purpose.

Initial access to the miniscope.org wiki was enabled mid January, 2016.

'''Important:''' Using this system we have successfully imaged Hippocampal CA1, Subiculum, Dorsal Striatum, Parietal Cortex, Prefrontal Cortex, and Visual Cortex using 0.5mm, 1mm, 1.8mm, and 2mm diameter GRIN lenses from either Grintech or GoFoton. (More information on GRIN lenses can be found [[GRIN Lens Information|here]]).

{{#ev:youtube|https://youtu.be/IEoXGuoc_pU|640|center}}

{{#ev:youtube|https://youtu.be/DCxTaPUPjN8|640|center}}

 

== Links to information on miniscope subsystems ==
[[File:Overview_System.png|thumb|600px]]
:[[Head Mounted Scope]]

:[[Data Acquisition Box]]

:[[Data Acquisition Software]]

:[[Surgery Protocol]]

:[https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing Master Parts List]

:[[Analysis Package]]

:[[GRIN Lens Information]]

 

== Discussion Board and FAQ ==
:[http://miniscope.org/board Discussion Board] (Our previous discussion board can be found [[Special:WikiForum|here.]]. Please do not post here)
:[[FAQs]]

== Guides and Tutorials==
A key feature of this effort is to design miniscope systems that are easy to build and use. The guides below will walk you through component procurement, scope assembly, and software installation.

# [[Overview of System Components]]
# [[Part Procurement]]
# [[System Assembly]]
# [[Recommended Computer Specs]]
# [[Software and Firmware Setup]]
# [[Initial Testing of Assembled Miniscopes]]
# [[Imaging With Thin GRIN Lenses]]
# [[Surgery Protocol]]
# [[Animal Behavior Guide]]

== Workshop Resource ==
We will be holding a pre-SfN workshop November 9th, 2017. For more information visit our [http://www.iclm.ucla.edu/page/MiniscopeWorkshopMCCS-ICLM.html MCCS/ICLM Workshop Page].

The Golshani, Silva, and Khakh labs will be hosting free, two-day long Miniscope workshops here at UCLA. We are currently planning at least 3 workshops for 2018. Please enter your information [https://goo.gl/forms/YXt8HeLpoeX2fVWz2 here] to request a spot in upcoming workshops.

<gallery widths=300px heights=200px mode="packed">
Image:Workshop_Jan2016.jpg|January 2016 Workshop
Image:Workshop_Mar2016.jpg|March 2016 Workshop
Image:Workshop_April2016.JPG|April 2016 Workshop
Image:UCLA_Worshop_June.JPG|UCLA Workshop, June 2016
Image:MCCS_Workshop_Nov2016.JPG|MCCS Miniscope Workshop, November 2016
</gallery>

'''If you cannot attend one of our workshops, presentations, data files, and workshop videos can be found on our [[Online Workshop]] page.'''

 

== Miniscope Community Member Pages ==
:[[Member Pages]]

== Update Log ==
;5/2/2017
:Updated 'Additional Open Source Resources' to include CNMF-E from the Paninski Lab and an open source miniature microscope from the Gardner Lab.
;2/01/2017
:Added additional assembly and surgery tutorial videos.
;11/29/2016
:Added a link on the front page to request a spot in upcoming Miniscope workshops.
;10/28/2016
:Added version 3.2 of the DAQ PCB to the GitHub repository.
;07/28/2016
:Added a new group PCB order signup sheet [https://docs.google.com/spreadsheets/d/1eXogU7JdeuhMHnVIJBHvCVjgZ6e9KnxPGWvJEBK-eyw/edit?usp=sharing here].
;07/21/2016
:Fixed bug that would crash the Miniscope DAQ software when using the 'Trigger Ext' option. This option is now fully functional and allows one to remotely trigger the Miniscope to record using a LVTTL or TTL high signal.
;04/20/2016
:Added [[Initial Testing of Assembled Miniscopes]] which outlines the process of testing new Miniscope systems.
;04/16/2016
:Added [[Imaging With Thin GRIN Lenses]] describing how to use Miniscopes to image with GRIN lenses 1mm diameter and thinner.
;04/12/2016
:Added a new group PCB order signup sheet [https://docs.google.com/spreadsheets/d/10_WgeJhZptxXbO2iEl93GyYGTDoEPvbrUjbIsegxpiI/edit?usp=sharing here].
;04/13/2016
:Updated the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB GitHub repository] to include the newer version of the CMOS Imaging Sensor PCB (v3.2).
;03/25/2016
:Updated the [https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Surgery and Baseplating Presentation] link.
:Updated the [[Recommended Computer Specs]] page... Apparently a MacBook Pro running Windows 8 doesn't always agree with the Miniscope system.
;03/18/2016
:Added the DAQ housing design files to our GitHub repository.
;03/16/2016
:Added a [[Member Pages]] page for sharing miniscope.org member created pages.
;02/24/2016
:Added a set of example Miniscope data to the [[Online Workshop|Workshop Resources]] page.
;02/17/2016
:Added a new way to connectorize the coaxial cable. This update includes a new PCB design on the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB GitHub repository] as well as an assembly video on the [[System Assembly]] page.
;02/10/2016
:Started adding videos to the [[Online Workshop|Workshop Resource]] and [[System Assembly]] page
;02/05/2016
:Updated the DAQ Software and Firmware to support FPS adjustment. The source code and compiled files can be found on our GitHub repository.
;02/03/2016
:Updated Surgery Tools on Miniscope Master Parts List
;01/28/2016
:Added PCB price quotes to reference when ordering PCB fabrication and assembly through Sierra Circuits. They can be found on the [[Part Procurement]] page.
;01/27/2016
:'''IMPORTANT''': Updated CMOS Imaging Sensor PCB Fabrication file to newest version
;01/20/2016
:Updated Surgery Tools on Miniscope Master Parts List
:Added GRIN lens specifications on [[GRIN Lens Information]] page
:Updated the PCB Assembly documents on Github will a more detailed description of SMD LED orientation
:Slight modification to the Baseplate 3D model on Github
;01/14/2016
:Comments added to segmentation functions
:Added through-hole components for DAQ PCB on Master Parts List
:Added additional soldering tools on Master Parts List
;01/13/2016
:Added basic surgery outline
:Added a picture guide for scope and Baseplate assembly
;01/12/2016
:Finalizing of Miniscope Master Parts List
;01/10/2016
:Upload of current version of all files and documents to Github
;01/09/2016
:Added guide to programming firmware to DAQ PCB

Online Workshop

2017-08-30T00:15:40Z

Tristanshuman: /* Image Acquisition and Lens Testing */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[[Initial Testing of Assembled Miniscopes]]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Online Workshop

2017-08-30T00:15:27Z

Tristanshuman: /* Image Acquisition and Lens Testing */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
[Initial Testing of Assembled Miniscopes]

=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

System Assembly

2017-08-30T00:13:26Z

Tristanshuman: /* Through-hole component assembly for version 2.x of PCB */

This guide will take you through the assembly of the entire miniscope system.

[[File:ScopeAssemblyParts.jpg|thumb|400px]]

== Head Mounted Scope Assembly ==
A detailed video is soon to come.

#Examine '''Main Body''' under a microscope and remove any plastic burrs and obstructions to the light paths.
#Press fit magnets into the 3 holes on the bottom of the '''Main Body''' making sure the polarity of the magnets match previously assembled scopes.
#Slide the '''Achromatic Lens''' down the emission path until it sits flush against the aperture ring above the emission filter slot. The more curved of the two sides of the lens should face down toward the emission filter. Inspect fit under microscope and adjust if necessary.
#With the coated surface facing the incoming light, use forceps to slide the ''Excitation Filter, Dichroic Mirror, and Emission Filter''' into their respective slots until their sides are flush with the Main Body. The black edges of the filters represent which edges should be blackened (optional).
#Place the '''Half-Ball Lens''' in spherical opening (optical glue is optional). Inspect under a microscope to make sure the lens surface is flush with the plastic. Screw the Excitation LED PCB in place using 1mm self-tapping screws.
#Screw the '''Filter Set Holder''' onto the '''Main Body''' using 2 to 3 1mm self-tapping screws.
#Slide the '''Focusing Slider''' onto the '''Main Body'''. '''Make sure the two side holes have been tapped already with a 00-80 tap'''.
#Epoxy, screw, or rubber band the '''CMOS Imaging Sensor PCB''' onto the '''Focusing Slider''' orienting the LED wires to the side of the scope with the '''Excitation LED PCB'''.

[[File:ScopeAssembly2.png|center|900px]]
 

{{#ev:youtube|https://youtu.be/p-RcVYbLlKc|640|center}}

 

=== Filter Edge Blackening (NOT USUALLY NECESSARY) ===
Our current version should not need this, but if you have light that leaks through the miniscope (i.e., you can see light being recorded even when the bottom of the miniscope is entirely covered), then blackening of the filters can fix this problem. We have noticed that if a scope has light leakage issues (excitation light making it to the CMOS imaging sensor) blackening the dichroic and emission filters' sides fixes the issue.

Optical companies may be able to blacken the sides for you but it is also easy to do yourself. We have had the most success using Rustoleum Flat Black Enamel with a thin paintbrush.
#Pour a few drops of the enamel into a plastic dish and let it sit out for a few minutes to thicken.
#Holding the sides of the filter with forceps carefully apply a thin layer of the enamel to the 2 sides not in contact with the forceps.
#Let dry for a few minutes before setting the filter down.
#Wait a couple hours for the enamel to dry further then repeat step 2 on the other 2 sides of the filter.

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering the solder-jumper on the bottom of the CMOS PCB (v3.2) ===
If you are using version 3.2 of the CMOS imaging sensor PCB you will need to apply solder across the two half-circles on the bottom of the PCB.

[[File:CMOS_Short_v3_2.png|center|600px]]

=== Soldering SMA Connector to Coaxial Cable ===
Below shows the easiest way to solder an SMA connector to the end of the coaxial cable. This can also be done using standard SMA wire connectors but it more difficult and more prone to breaks. '''Make sure to test for shorts in the coax cable before plugging in and powering up the DAQ PCB. If a short is present, permanent damage can be done to the DAQ PCB.'''

{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering LED to PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

'''Removing the silicone cover of the LED:''' try to slowly peal it off in 1 piece and make sure not to touch the white square (illumination surface) with forceps. It is fine to leave a small amount of silicone attached to the LED as long as it does not extend much higher than the actual surface of the LED.

=== Soldering LED power lines ===
[[File:LEDWire.png|thumb|300px]]
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

'''Soldering the LED wires to the LED PCB:''' Once the LED PCB is attached to the scope body, the wires running off the LED PCB need to fit through a thin slot cut out of the scope body. This slot is only the width of the 2 solder pads on the LED PCB so care should be taken to solder the wires directly on top of the solder pads and have the wires extend straight off the PCB. It is helpful to use relatively thin wires, ideally with and outer diameter of 0.5mm or less.

=== Baseplate Assembly ===
#Inspect Baseplate for burrs.
#Press fit the 3 magnets flush or slightly recessed into the Baseplate.
#Tap the set screw hole with a 00-80 tap.

[[File:BaseplateAssembly.png|center|400px]]

== Data Acquisition System Assembly ==

=== Note on version 3.x of the DAQ PCB ===
If you have the newer version of the DAQ PCB (version 3.x) you can disregard the through-hole and coax cable connector soldering described below. The DAQ PCB v3.x comes fully soldered and just needs the EEPROM inserted and switch/jumper configuration set correctly. The coaxial cable from the head mounted scope will connect to the J4 (SMA connector closest to the center of the DAQ PCB) connector.

[[File:DAQv3_x.png|center|500px]]

=== Through-hole component assembly for version 2.x of PCB (USUALLY NOT NEEDED) ===
If you decide to have the through-hole components assembled by an assembly house you can skip this section. Below is a picture highlighting the necessary through-hole components that need to be soldered in order for the DAQ PCB to function properly.

[[File:DAQPCBThroughHole.png|center|500px]]

*Description of components
**SW4: Reset button the resets can reset the USB Host Controller
**U5: EEPROM (memory that holds the DAQ firmware) socket. You can also solder the EEPROM IC directly to the board but I prefer using an IC socket so I can swap out the EEPROM if necessary
**K1,2,3: Each are 2pin 0.1" headers
**J9: A 3pin header used with a 2pin jumper to select power source for the microscope
**J3,4,5: SMA connectors used for GPIO pins
**J6: We currently solder a short coax cable with SMA connector to these pads. This will be updated soon to a replace this with a proper PCB footprint
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Plugging in EEPROM ===
Plug in the EEPROM into socket U5 making sure the orientation is correct (With the USB connector on the bottom the writing on the EEPROM should be right side up).

[[File:EEPROM_Ori.png|center|500px]]

=== Setting Jumpers ===
Once all SMD and through-hole components are in place the switches and jumpers need to be properly set for uploading firmware and powering the microscope.

Below shows the default configuration of the 3 SMD switches on the DAQ PCB.

[[File:SwitchSettings.png|center|500px]]

Below shows the possible K1, K2, and K3 jumper configurations.

[[File:BootMode.png|center|500px]]

The scope power jumper, J9, sets the power source powering the head mounted scope. In most cases the USB power configuration should be used and no DC power supply needs to be hooked up the the DC jack on the PCB.

[[File:PowerJumper.png|center|500px]]

=== Epoxy USB Connector ===
If a USB cable is forced in or pulled out of the USB connector at an angle there is a chance the connector could get ripped off the PCB. While not necessary, we suggest adding epoxy between the USB connector housing and PCB to increase its mechanical stability and decrease the chances of damage. Care must be taken to avoid getting any epoxy inside the USB housing.

== Cable Assembly ==
The cabling between the head mounted scope and DAQ hardware is only a single coaxial cable. A coaxial, or coax, cable consists of an inner conducting wire surrounded by an insulating dielectric and then outer, generally grounded, shield. In our system the inner conductor carries power along with a data link and bidirectional control channel and the outer shield needs to be grounded. Our hardware dynamically adjusts for signal attenuation and small voltage drops across the cable but care should still be taken to minimize these loses. The videos above show how to solder the coax cable to the CMOS Imaging Sensor PCB and how to connectorize the other end with an SMA connector. Suggested cable can be found on our parts list but any coax cable with the properties listed below should work.

Properties to look for in a coax cable are
*50ohm impedance. This is absolutely necessary.
*Light weight and highly flexible. We like to use coax cables with an outer diameter of 1.5mm or less. It is important to note that as the diameter of the cable decreases, so does the length it can support.
*Handles bandwidths up to 1GHz. For short distances this requirement can be reduced.

== What to do After System Assembly ==
[[Software and Firmware Setup]]

[[Initial Testing of Assembled Miniscopes]]

System Assembly

2017-08-30T00:07:35Z

Tristanshuman: /* Filter Edge Blackening (Suggested) */

This guide will take you through the assembly of the entire miniscope system.

[[File:ScopeAssemblyParts.jpg|thumb|400px]]

== Head Mounted Scope Assembly ==
A detailed video is soon to come.

#Examine '''Main Body''' under a microscope and remove any plastic burrs and obstructions to the light paths.
#Press fit magnets into the 3 holes on the bottom of the '''Main Body''' making sure the polarity of the magnets match previously assembled scopes.
#Slide the '''Achromatic Lens''' down the emission path until it sits flush against the aperture ring above the emission filter slot. The more curved of the two sides of the lens should face down toward the emission filter. Inspect fit under microscope and adjust if necessary.
#With the coated surface facing the incoming light, use forceps to slide the ''Excitation Filter, Dichroic Mirror, and Emission Filter''' into their respective slots until their sides are flush with the Main Body. The black edges of the filters represent which edges should be blackened (optional).
#Place the '''Half-Ball Lens''' in spherical opening (optical glue is optional). Inspect under a microscope to make sure the lens surface is flush with the plastic. Screw the Excitation LED PCB in place using 1mm self-tapping screws.
#Screw the '''Filter Set Holder''' onto the '''Main Body''' using 2 to 3 1mm self-tapping screws.
#Slide the '''Focusing Slider''' onto the '''Main Body'''. '''Make sure the two side holes have been tapped already with a 00-80 tap'''.
#Epoxy, screw, or rubber band the '''CMOS Imaging Sensor PCB''' onto the '''Focusing Slider''' orienting the LED wires to the side of the scope with the '''Excitation LED PCB'''.

[[File:ScopeAssembly2.png|center|900px]]
 

{{#ev:youtube|https://youtu.be/p-RcVYbLlKc|640|center}}

 

=== Filter Edge Blackening (NOT USUALLY NECESSARY) ===
Our current version should not need this, but if you have light that leaks through the miniscope (i.e., you can see light being recorded even when the bottom of the miniscope is entirely covered), then blackening of the filters can fix this problem. We have noticed that if a scope has light leakage issues (excitation light making it to the CMOS imaging sensor) blackening the dichroic and emission filters' sides fixes the issue.

Optical companies may be able to blacken the sides for you but it is also easy to do yourself. We have had the most success using Rustoleum Flat Black Enamel with a thin paintbrush.
#Pour a few drops of the enamel into a plastic dish and let it sit out for a few minutes to thicken.
#Holding the sides of the filter with forceps carefully apply a thin layer of the enamel to the 2 sides not in contact with the forceps.
#Let dry for a few minutes before setting the filter down.
#Wait a couple hours for the enamel to dry further then repeat step 2 on the other 2 sides of the filter.

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering the solder-jumper on the bottom of the CMOS PCB (v3.2) ===
If you are using version 3.2 of the CMOS imaging sensor PCB you will need to apply solder across the two half-circles on the bottom of the PCB.

[[File:CMOS_Short_v3_2.png|center|600px]]

=== Soldering SMA Connector to Coaxial Cable ===
Below shows the easiest way to solder an SMA connector to the end of the coaxial cable. This can also be done using standard SMA wire connectors but it more difficult and more prone to breaks. '''Make sure to test for shorts in the coax cable before plugging in and powering up the DAQ PCB. If a short is present, permanent damage can be done to the DAQ PCB.'''

{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering LED to PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

'''Removing the silicone cover of the LED:''' try to slowly peal it off in 1 piece and make sure not to touch the white square (illumination surface) with forceps. It is fine to leave a small amount of silicone attached to the LED as long as it does not extend much higher than the actual surface of the LED.

=== Soldering LED power lines ===
[[File:LEDWire.png|thumb|300px]]
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

'''Soldering the LED wires to the LED PCB:''' Once the LED PCB is attached to the scope body, the wires running off the LED PCB need to fit through a thin slot cut out of the scope body. This slot is only the width of the 2 solder pads on the LED PCB so care should be taken to solder the wires directly on top of the solder pads and have the wires extend straight off the PCB. It is helpful to use relatively thin wires, ideally with and outer diameter of 0.5mm or less.

=== Baseplate Assembly ===
#Inspect Baseplate for burrs.
#Press fit the 3 magnets flush or slightly recessed into the Baseplate.
#Tap the set screw hole with a 00-80 tap.

[[File:BaseplateAssembly.png|center|400px]]

== Data Acquisition System Assembly ==

=== Note on version 3.x of the DAQ PCB ===
If you have the newer version of the DAQ PCB (version 3.x) you can disregard the through-hole and coax cable connector soldering described below. The DAQ PCB v3.x comes fully soldered and just needs the EEPROM inserted and switch/jumper configuration set correctly. The coaxial cable from the head mounted scope will connect to the J4 (SMA connector closest to the center of the DAQ PCB) connector.

[[File:DAQv3_x.png|center|500px]]

=== Through-hole component assembly for version 2.x of PCB ===
If you decide to have the through-hole components assembled by an assembly house you can skip this section. Below is a picture highlighting the necessary through-hole components that need to be soldered in order for the DAQ PCB to function properly.

[[File:DAQPCBThroughHole.png|center|500px]]

*Description of components
**SW4: Reset button the resets can reset the USB Host Controller
**U5: EEPROM (memory that holds the DAQ firmware) socket. You can also solder the EEPROM IC directly to the board but I prefer using an IC socket so I can swap out the EEPROM if necessary
**K1,2,3: Each are 2pin 0.1" headers
**J9: A 3pin header used with a 2pin jumper to select power source for the microscope
**J3,4,5: SMA connectors used for GPIO pins
**J6: We currently solder a short coax cable with SMA connector to these pads. This will be updated soon to a replace this with a proper PCB footprint
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Plugging in EEPROM ===
Plug in the EEPROM into socket U5 making sure the orientation is correct (With the USB connector on the bottom the writing on the EEPROM should be right side up).

[[File:EEPROM_Ori.png|center|500px]]

=== Setting Jumpers ===
Once all SMD and through-hole components are in place the switches and jumpers need to be properly set for uploading firmware and powering the microscope.

Below shows the default configuration of the 3 SMD switches on the DAQ PCB.

[[File:SwitchSettings.png|center|500px]]

Below shows the possible K1, K2, and K3 jumper configurations.

[[File:BootMode.png|center|500px]]

The scope power jumper, J9, sets the power source powering the head mounted scope. In most cases the USB power configuration should be used and no DC power supply needs to be hooked up the the DC jack on the PCB.

[[File:PowerJumper.png|center|500px]]

=== Epoxy USB Connector ===
If a USB cable is forced in or pulled out of the USB connector at an angle there is a chance the connector could get ripped off the PCB. While not necessary, we suggest adding epoxy between the USB connector housing and PCB to increase its mechanical stability and decrease the chances of damage. Care must be taken to avoid getting any epoxy inside the USB housing.

== Cable Assembly ==
The cabling between the head mounted scope and DAQ hardware is only a single coaxial cable. A coaxial, or coax, cable consists of an inner conducting wire surrounded by an insulating dielectric and then outer, generally grounded, shield. In our system the inner conductor carries power along with a data link and bidirectional control channel and the outer shield needs to be grounded. Our hardware dynamically adjusts for signal attenuation and small voltage drops across the cable but care should still be taken to minimize these loses. The videos above show how to solder the coax cable to the CMOS Imaging Sensor PCB and how to connectorize the other end with an SMA connector. Suggested cable can be found on our parts list but any coax cable with the properties listed below should work.

Properties to look for in a coax cable are
*50ohm impedance. This is absolutely necessary.
*Light weight and highly flexible. We like to use coax cables with an outer diameter of 1.5mm or less. It is important to note that as the diameter of the cable decreases, so does the length it can support.
*Handles bandwidths up to 1GHz. For short distances this requirement can be reduced.

== What to do After System Assembly ==
[[Software and Firmware Setup]]

[[Initial Testing of Assembled Miniscopes]]

Online Workshop

2017-08-29T23:59:22Z

Tristanshuman: /* Hands-on Workstations */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==

[https://drive.google.com/file/d/0B4EiRp6ZxCg3WHVNU1VVd3lsZWc/view?usp=sharing Worksheet - Soldering]

=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Online Workshop

2017-08-29T23:55:04Z

Tristanshuman: /* In Vivo Imaging and Behavior */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing Worksheet - In Vivo Imaging and Behavior Tips]

Online Workshop

2017-08-29T23:54:47Z

Tristanshuman: /* Assembly of Miniscopes */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Worksheet - Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing In Vivo Imaging and Behavior Tips Doc]

Online Workshop

2017-08-29T23:53:52Z

Tristanshuman: /* Image Processing and Analysis */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 Powerpoint - Image Processing and Analysis]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing In Vivo Imaging and Behavior Tips Doc]

Online Workshop

2017-08-29T23:52:03Z

Tristanshuman: /* Surgery Procedure and Baseplating */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Powerpoint - Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 | Image Processing and Analysis Powerpoint]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing In Vivo Imaging and Behavior Tips Doc]

Online Workshop

2017-08-29T23:51:50Z

Tristanshuman: /* Imaging Principles and Microscope Design */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint - Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 | Image Processing and Analysis Powerpoint]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing In Vivo Imaging and Behavior Tips Doc]

Online Workshop

2017-08-29T23:51:27Z

Tristanshuman: /* Imaging Principles and Microscope Design */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Imaging Principles and Microscope Design]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 | Image Processing and Analysis Powerpoint]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing In Vivo Imaging and Behavior Tips Doc]

Main Page

2017-08-29T23:48:28Z

Tristanshuman:

[[File:miniscopev2.JPG|thumb|300px]]
'''Welcome to Miniscope.org Wiki! Follow the project on Twitter: [https://twitter.com/MiniscopeTeam @MiniscopeTeam].'''

The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Stanford and published in a [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1694.html paper in Nature Methods in 2011]. It uses wide-field fluorescence imaging to record neural activity in awake, freely moving mice. The microscope introduced here (Miniscope) has a mass of 3 grams and uses a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data to custom open source Data Acquisition (DAQ) hardware and software. This wiki site provides a centralized location for sharing design files, source code, and other relevant information so that a community of users can share ideas and developments related to this important imaging technique. Our goal is to help disseminate this technology to the larger neuroscience community and build a foundation of users that will continue advancing this technology and contribute back to the project. While the Miniscope system described here is not an off-the-shelf commercial solution, we have focused on making it as easy as possible for the average neuroscience lab to build and modify, requiring minimal soldering and hands on assembly. For more information please visit the [[Overview of System Components|Project Overview]] page. The Miniscope project and Miniscope.org are still works in progress and will be routinely updated over the coming months and years. We hope you will contribute to this important process!

== Current Status of Project ==
The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. Miniscopes were used to understand how the brain links memories across time, with the findings published in [http://www.nature.com/nature/journal/v534/n7605/full/nature17955.html Nature, 2016]. The work and files available on this site are the most up-to-date public version of our system and will be updated frequently with improvements and new system features. Again, we hope that you will contribute to this development process! This wiki is designed for this very purpose.

Initial access to the miniscope.org wiki was enabled mid January, 2016.

'''Important:''' Using this system we have successfully imaged Hippocampal CA1, Subiculum, Dorsal Striatum, and Visual Cortex using 1.8mm and 2mm diameter GRIN lenses from Grintech. While thinner GRIN lenses should theoretically be compatible with our system we have limited our initial development to larger lenses due to supply and experimental constraints. We are now actively testing thinner lenses as well as pursuing multiple avenues of GRIN lens production (More information on GRIN lenses can be found [[GRIN Lens Information|here]]).

{{#ev:youtube|https://youtu.be/IEoXGuoc_pU|640|center}}

{{#ev:youtube|https://youtu.be/DCxTaPUPjN8|640|center}}

 

== Links to information on miniscope subsystems ==
[[File:Overview_System.png|thumb|600px]]
:[[Head Mounted Scope]]

:[[Data Acquisition Box]]

:[[Data Acquisition Software]]

:[[Surgery Protocol]]

:[https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing Master Parts List]

:[[Analysis Package]]

:[[GRIN Lens Information]]

 

== Discussion Board and FAQ ==
:[http://miniscope.org/board Discussion Board] (Our previous discussion board can be found [[Special:WikiForum|here.]]. Please do not post here)
:[[FAQs]]

== Guides and Tutorials==
A key feature of this effort is to design miniscope systems that are easy to build and use. The guides below will walk you through component procurement, scope assembly, and software installation.

# [[Overview of System Components]]
# [[Part Procurement]]
# [[System Assembly]]
# [[Recommended Computer Specs]]
# [[Software and Firmware Setup]]
# [[Initial Testing of Assembled Miniscopes]]
# [[Imaging With Thin GRIN Lenses]]
# [[Surgery Protocol]]
# [[Animal Behavior Guide]]

== Workshop Resource ==
We will be holding a pre-SfN workshop November 9th, 2017. For more information visit our [http://www.iclm.ucla.edu/page/MiniscopeWorkshopMCCS-ICLM.html MCCS/ICLM Workshop Page].

The Golshani, Silva, and Khakh labs will be hosting free, two-day long Miniscope workshops here at UCLA. We are currently planning at least 3 workshops for 2018. Please enter your information [https://goo.gl/forms/YXt8HeLpoeX2fVWz2 here] to request a spot in upcoming workshops.

<gallery widths=300px heights=200px mode="packed">
Image:Workshop_Jan2016.jpg|January 2016 Workshop
Image:Workshop_Mar2016.jpg|March 2016 Workshop
Image:Workshop_April2016.JPG|April 2016 Workshop
Image:UCLA_Worshop_June.JPG|UCLA Workshop, June 2016
Image:MCCS_Workshop_Nov2016.JPG|MCCS Miniscope Workshop, November 2016
</gallery>

'''If you cannot attend one of our workshops, presentations, data files, and workshop videos can be found on our [[Online Workshop]] page.'''

 

== Miniscope Community Member Pages ==
:[[Member Pages]]

== Update Log ==
;5/2/2017
:Updated 'Additional Open Source Resources' to include CNMF-E from the Paninski Lab and an open source miniature microscope from the Gardner Lab.
;2/01/2017
:Added additional assembly and surgery tutorial videos.
;11/29/2016
:Added a link on the front page to request a spot in upcoming Miniscope workshops.
;10/28/2016
:Added version 3.2 of the DAQ PCB to the GitHub repository.
;07/28/2016
:Added a new group PCB order signup sheet [https://docs.google.com/spreadsheets/d/1eXogU7JdeuhMHnVIJBHvCVjgZ6e9KnxPGWvJEBK-eyw/edit?usp=sharing here].
;07/21/2016
:Fixed bug that would crash the Miniscope DAQ software when using the 'Trigger Ext' option. This option is now fully functional and allows one to remotely trigger the Miniscope to record using a LVTTL or TTL high signal.
;04/20/2016
:Added [[Initial Testing of Assembled Miniscopes]] which outlines the process of testing new Miniscope systems.
;04/16/2016
:Added [[Imaging With Thin GRIN Lenses]] describing how to use Miniscopes to image with GRIN lenses 1mm diameter and thinner.
;04/12/2016
:Added a new group PCB order signup sheet [https://docs.google.com/spreadsheets/d/10_WgeJhZptxXbO2iEl93GyYGTDoEPvbrUjbIsegxpiI/edit?usp=sharing here].
;04/13/2016
:Updated the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB GitHub repository] to include the newer version of the CMOS Imaging Sensor PCB (v3.2).
;03/25/2016
:Updated the [https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Surgery and Baseplating Presentation] link.
:Updated the [[Recommended Computer Specs]] page... Apparently a MacBook Pro running Windows 8 doesn't always agree with the Miniscope system.
;03/18/2016
:Added the DAQ housing design files to our GitHub repository.
;03/16/2016
:Added a [[Member Pages]] page for sharing miniscope.org member created pages.
;02/24/2016
:Added a set of example Miniscope data to the [[Online Workshop|Workshop Resources]] page.
;02/17/2016
:Added a new way to connectorize the coaxial cable. This update includes a new PCB design on the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB GitHub repository] as well as an assembly video on the [[System Assembly]] page.
;02/10/2016
:Started adding videos to the [[Online Workshop|Workshop Resource]] and [[System Assembly]] page
;02/05/2016
:Updated the DAQ Software and Firmware to support FPS adjustment. The source code and compiled files can be found on our GitHub repository.
;02/03/2016
:Updated Surgery Tools on Miniscope Master Parts List
;01/28/2016
:Added PCB price quotes to reference when ordering PCB fabrication and assembly through Sierra Circuits. They can be found on the [[Part Procurement]] page.
;01/27/2016
:'''IMPORTANT''': Updated CMOS Imaging Sensor PCB Fabrication file to newest version
;01/20/2016
:Updated Surgery Tools on Miniscope Master Parts List
:Added GRIN lens specifications on [[GRIN Lens Information]] page
:Updated the PCB Assembly documents on Github will a more detailed description of SMD LED orientation
:Slight modification to the Baseplate 3D model on Github
;01/14/2016
:Comments added to segmentation functions
:Added through-hole components for DAQ PCB on Master Parts List
:Added additional soldering tools on Master Parts List
;01/13/2016
:Added basic surgery outline
:Added a picture guide for scope and Baseplate assembly
;01/12/2016
:Finalizing of Miniscope Master Parts List
;01/10/2016
:Upload of current version of all files and documents to Github
;01/09/2016
:Added guide to programming firmware to DAQ PCB

Online Workshop

2017-05-19T10:31:03Z

Tristanshuman: /* Assembly of Miniscopes */

This page will contain videos of everything presented at our in-person workshops (Will be updated shortly).
== Imaging Principles and Microscope Design ==
[https://www.dropbox.com/s/ro4n7qb27ogny4g/Workshop%20Imaging%20Principles%20and%20Microscope%20Design.pptx?dl=0 Powerpoint Presentation]

== Surgery Procedure and Baseplating ==
[https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Surgery and Baseplating Presentation]

== Image Processing and Analysis==
[https://drive.google.com/a/g.ucla.edu/folderview?id=0B-x_dM_VK0wKeDZnYlRBTHVIOGs&usp=sharing| Sample Imaging Data]

[https://www.dropbox.com/s/d5y8o1nghf785iw/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx?dl=0 | Image Processing and Analysis Powerpoint]

== Hands-on Workstations ==
=== Soldering Coaxial Cable to CMOS Imaging Sensor PCB ===
{{#ev:youtube|https://youtu.be/aXzErQn3U7g|640|center}}

=== Soldering SMA Connector to Coaxial Cable ===
{{#ev:youtube|https://youtu.be/Jrn2oWERPpw|640|center}}

=== Soldering Male SMA Connector/Cable to DAQ PCB v2.01 ===
This connector will be changed to a through-hole SMA connector in a future version of the DAQ PCB. For version 2.01 DAQ PCBs follow the steps shown in the video below.
{{#ev:youtube|https://youtu.be/-BMkPaSKkk8|640|center}}

=== Soldering LED onto LED PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

=== Soldering LED wires to PCBs ===
{{#ev:youtube|https://youtu.be/AWg9-qTKF1Y|640|center}}

=== Assembly of Miniscopes ===
[https://docs.google.com/document/d/1fnVXbNp4Gjp_bCMBMAxIDmJZz87G7ROGn2iPIN19Vms/edit?usp=sharing Head Mounted Scope Assembly]

=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===
[https://docs.google.com/document/d/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/edit?usp=sharing In Vivo Imaging and Behavior Tips Doc]

Contributors

2016-11-29T00:23:21Z

Tristanshuman: /* Techs */

This project is a collaboration between the Golshani Lab, Silva Lab, and Khakh Lab at the University of California, Los Angeles.

== Principal Investigators ==
;Peyman Golshani
:Department of Neurology at David Geffen School of Medicine, UCLA


;Alcino Silva
:Neurobiology, Psychiatry and Psychology, UCLA


;Baljit Khakh
:Physiology and Neurobiology, UCLA


== Postdocs ==
;Daniel Aharoni
:Golshani, Silva, and Khakh Lab, UCLA
:DAharoni@mednet.ucla.edu
;Tristan Shuman
:Golshani Lab, UCLA
:tristanshuman@gmail.com
;Denise Cai
:Silva Lab, UCLA
:denisecai@gmail.com
;Tsai-Yi Lu
:Khakh Lab, UCLA
:tsaiyilu@gmail.com

== Research Technicians ==
;Christopher Lee
:Golshani Lab, UCLA
;Mimi La-Vu
:Silva Lab, UCLA
;Sergio Flores
:Golshani Lab, UCLA

== Graduate Students ==

==Undergraduate Students ==

Contributors

2016-11-29T00:22:50Z

Tristanshuman: /* Techs */

This project is a collaboration between the Golshani Lab, Silva Lab, and Khakh Lab at the University of California, Los Angeles.

== Principal Investigators ==
;Peyman Golshani
:Department of Neurology at David Geffen School of Medicine, UCLA


;Alcino Silva
:Neurobiology, Psychiatry and Psychology, UCLA


;Baljit Khakh
:Physiology and Neurobiology, UCLA


== Postdocs ==
;Daniel Aharoni
:Golshani, Silva, and Khakh Lab, UCLA
:DAharoni@mednet.ucla.edu
;Tristan Shuman
:Golshani Lab, UCLA
:tristanshuman@gmail.com
;Denise Cai
:Silva Lab, UCLA
:denisecai@gmail.com
;Tsai-Yi Lu
:Khakh Lab, UCLA
:tsaiyilu@gmail.com

== Techs ==
;Christopher Lee
:Golshani Lab, UCLA
;Mimi La-Vu
:Silva Lab, UCLA
;Sergio Flores
:Golshani Lab, UCLA

== Graduate Students ==

==Undergraduate Students ==

Main Page

2016-11-29T00:21:03Z

Tristanshuman: /* Workshop Resource */

[[File:miniscopev2.JPG|thumb|300px]]
'''Welcome to Miniscope.org Wiki! Follow the project on Twitter: [https://twitter.com/UclaMiniscope @UclaMiniscope].'''

The miniature fluorescence microscope described here is based on a design pioneered by Mark Schnitzer's Lab at Stanford and published in a [http://www.nature.com/nmeth/journal/v8/n10/full/nmeth.1694.html paper in Nature Methods in 2011]. It uses wide-field fluorescence imaging to record neural activity in awake, freely moving mice. The microscope introduced here (Miniscope) has a mass of 3 grams and uses a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data to custom open source Data Acquisition (DAQ) hardware and software. This wiki site provides a centralized location for sharing design files, source code, and other relevant information so that a community of users can share ideas and developments related to this important imaging technique. Our goal is to help disseminate this technology to the larger neuroscience community and build a foundation of users that will continue advancing this technology and contribute back to the project. While the Miniscope system described here is not an off-the-shelf commercial solution, we have focused on making it as easy as possible for the average neuroscience lab to build and modify, requiring minimal soldering and hands on assembly. For more information please visit the [[Overview of System Components|Project Overview]] page. The Miniscope project and Miniscope.org are still works in progress and will be routinely updated over the coming months and years. We hope you will contribute to this important process!

== Current Status of Project ==
The Miniscope project is now in its third year of development at UCLA and has gone through two major revisions. Miniscopes were used to understand how the brain links memories across time, with the findings published in [http://www.nature.com/nature/journal/v534/n7605/full/nature17955.html Nature, 2016]. The work and files available on this site are the most up-to-date public version of our system and will be updated frequently with improvements and new system features. Again, we hope that you will contribute to this development process! This wiki is designed for this very purpose.

Initial access to the miniscope.org wiki was enabled mid January, 2016.

'''Important:''' Using this system we have successfully imaged Hippocampal CA1, Subiculum, Dorsal Striatum, and Visual Cortex using 1.8mm and 2mm diameter GRIN lenses from Grintech. While thinner GRIN lenses should theoretically be compatible with our system we have limited our initial development to larger lenses due to supply and experimental constraints. We are now actively testing thinner lenses as well as pursuing multiple avenues of GRIN lens production (More information on GRIN lenses can be found [[GRIN Lens Information|here]]).

{{#ev:youtube|https://youtu.be/IEoXGuoc_pU|640|center}}

{{#ev:youtube|https://youtu.be/DCxTaPUPjN8|640|center}}

 

== Links to information on miniscope subsystems ==
[[File:Overview_System.png|thumb|600px]]
:[[Head Mounted Scope]]

:[[Data Acquisition Box]]

:[[Data Acquisition Software]]

:[[Surgery Protocol]]

:[https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing Master Parts List]

:[[Analysis Package]]

:[[GRIN Lens Information]]

 

== Discussion Board and FAQ ==
:[http://miniscope.org/board Discussion Board] (Our previous discussion board can be found [[Special:WikiForum|here.]]. Please do not post here)
:[[FAQs]]

== Guides and Tutorials==
A key feature of this effort is to design miniscope systems that are easy to build and use. The guides below will walk you through component procurement, scope assembly, and software installation.

# [[Overview of System Components]]
# [[Part Procurement]]
# [[System Assembly]]
# [[Recommended Computer Specs]]
# [[Software and Firmware Setup]]
# [[Initial Testing of Assembled Miniscopes]]
# [[Imaging With Thin GRIN Lenses]]
# [[Surgery Protocol]]
# [[Animal Behavior Guide]]

== Workshop Resource ==
The Golshani, Silva, and Khakh labs will be hosting free, two-day long miniscope workshops here at UCLA. The next scheduled UCLA workshop is completely full but we are working on setting up more in the near future. We will update this page when more information is available.

<gallery widths=300px heights=200px mode="packed">
Image:Workshop_Jan2016.jpg|January 2016 Workshop
Image:Workshop_Mar2016.jpg|March 2016 Workshop
Image:Workshop_April2016.JPG|April 2016 Workshop
Image:UCLA_Worshop_June.JPG|UCLA Workshop, June 2016
</gallery>

'''If you cannot attend one of our workshops, presentations, data files, and workshop videos can be found on our [[Online Workshop]] page.'''

 

== Miniscope Community Member Pages ==
:[[Member Pages]]

== Update Log ==
;10/28/2016
:Added version 3.2 of the DAQ PCB to the GitHub repository.
;07/28/2016
:Added a new group PCB order signup sheet [https://docs.google.com/spreadsheets/d/1eXogU7JdeuhMHnVIJBHvCVjgZ6e9KnxPGWvJEBK-eyw/edit?usp=sharing here].
;07/21/2016
:Fixed bug that would crash the Miniscope DAQ software when using the 'Trigger Ext' option. This option is now fully functional and allows one to remotely trigger the Miniscope to record using a LVTTL or TTL high signal.
;04/20/2016
:Added [[Initial Testing of Assembled Miniscopes]] which outlines the process of testing new Miniscope systems.
;04/16/2016
:Added [[Imaging With Thin GRIN Lenses]] describing how to use Miniscopes to image with GRIN lenses 1mm diameter and thinner.
;04/12/2016
:Added a new group PCB order signup sheet [https://docs.google.com/spreadsheets/d/10_WgeJhZptxXbO2iEl93GyYGTDoEPvbrUjbIsegxpiI/edit?usp=sharing here].
;04/13/2016
:Updated the [https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB GitHub repository] to include the newer version of the CMOS Imaging Sensor PCB (v3.2).
;03/25/2016
:Updated the [https://drive.google.com/file/d/0ByUbjrn9MxK0TWdxUVVjakF3cDQ/view?usp=sharing| Surgery and Baseplating Presentation] link.
:Updated the [[Recommended Computer Specs]] page... Apparently a MacBook Pro running Windows 8 doesn't always agree with the Miniscope system.
;03/18/2016
:Added the DAQ housing design files to our GitHub repository.
;03/16/2016
:Added a [[Member Pages]] page for sharing miniscope.org member created pages.
;02/24/2016
:Added a set of example Miniscope data to the [[Online Workshop|Workshop Resources]] page.
;02/17/2016
:Added a new way to connectorize the coaxial cable. This update includes a new PCB design on the [https://github.com/daharoni/Miniscope_Coax_2_SMA_PCB GitHub repository] as well as an assembly video on the [[System Assembly]] page.
;02/10/2016
:Started adding videos to the [[Online Workshop|Workshop Resource]] and [[System Assembly]] page
;02/05/2016
:Updated the DAQ Software and Firmware to support FPS adjustment. The source code and compiled files can be found on our GitHub repository.
;02/03/2016
:Updated Surgery Tools on Miniscope Master Parts List
;01/28/2016
:Added PCB price quotes to reference when ordering PCB fabrication and assembly through Sierra Circuits. They can be found on the [[Part Procurement]] page.
;01/27/2016
:'''IMPORTANT''': Updated CMOS Imaging Sensor PCB Fabrication file to newest version
;01/20/2016
:Updated Surgery Tools on Miniscope Master Parts List
:Added GRIN lens specifications on [[GRIN Lens Information]] page
:Updated the PCB Assembly documents on Github will a more detailed description of SMD LED orientation
:Slight modification to the Baseplate 3D model on Github
;01/14/2016
:Comments added to segmentation functions
:Added through-hole components for DAQ PCB on Master Parts List
:Added additional soldering tools on Master Parts List
;01/13/2016
:Added basic surgery outline
:Added a picture guide for scope and Baseplate assembly
;01/12/2016
:Finalizing of Miniscope Master Parts List
;01/10/2016
:Upload of current version of all files and documents to Github
;01/09/2016
:Added guide to programming firmware to DAQ PCB

Surgery Protocol

2016-03-26T01:47:20Z

Tristanshuman:

Surgery Protocol

2016-03-26T01:46:26Z

Tristanshuman:

Surgery Protocol

2016-03-25T18:59:45Z

Tristanshuman:

The following is a basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging. For videos of surgery and baseplating, see the [[Online Workshop]].

In order to image, animals will need to undergo three surgical procedures: a virus injection, a GRIN lens implantation, and baseplate attachment.

== Virus Injection ==
Before implanting the GRIN lens, you will need to inject a fluorescent indicator such as GCaMP6. We have generally used AAV1.Syn.GCaMP6f.WPRE.SV40 from Penn Vector (Item number AV-1-PV2822) and had great success in dorsal CA1. You may also be able to use GCaMP6 transgenic mice, but we have not tested whether any of the newer lines are bright enough to be imaged.

== GRIN Lens Implantation==

=== Basic Equipment Needed ===
You will only need basic surgical equipment to perform GRIN lens implantation surgeries. This includes a mouse stereotax, an isoflurane vaporizor, surgical heat pad, stereo surgical microscope, light source, dental drill, and bead sterilizer. For recommended equipment, see the master [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].

You will need the following basic tools and supplies: fine forceps, blunt forceps, fine scissors, scalpel and blade, small skull screws, drill bits, cyanoacrylate glue, dental cement, Kwik-Sil, and [[cortex buffer]]

=== Aspirator and Lens Holder ===
You will need an aspirator to remove cortex above the hippocampus. This can be build very simply with a vacuum line (or pump), a liquid trap, 1 ml syringe (with a hole to control suction), blunt needles, tubing and connectors, and hot glue.
[[File:Aspirator.PNG|center|500px]]

You can easily build a GRIN lens holder by using a suction system to hold the lens in place as it is dropped into the brain for implantation. To build, start with two 1ml micropipette tips. Cut the first so that the tip is just larger than the diameter of the GRIN lens you will be using. Cut the second tip so that the end is just smaller than the size of the GRIN lens. Connect this end to a 1ml syringe and connect to a vacuum line. This will then hold the lens in place during implantation. You can then use tape to attach this holder to a stereotax. Another solution we have used is a basic drill chuck, but this is only good for large (2mm) lenses.
[[File:LensHolder.PNG|center|500px]]

=== Skull Preparation ===
You must first prepare the skull for implantation. We recommend shaving the head area and sterilizing with 3 alternating betadine and ethanol scrubs. Next, remove the scalp with scissors and clean the skull with hydrogen peroxide and saline. Scrape and score the skull to increase the bond with the glue. We also detach the neck muscle from the skull in order to reduce pull on the skull and prevent muscle growth that can make the implant less stable. Finally we insert a skull screw on the opposite side of the skull to enhance the stability of the implant.

=== Craniotomy and Aspiration ===
Using a stereotax, align the skull and find the location for the implant. Using a drill, make 4 guide holes to outline the lens placement. For CA1, we recommend offsetting the lens 0.5mm to the medial side of the virus injection to prevent imaging any damage induced by the virus injection. Connect the guide holes to create a circular craniotomy and peel off the circular skull fragment. Do not worry about blood as the top layers of cortex will be removed by aspiration. Make absolutely sure that the craniotomy is at least the size of your GRIN lens! Cover with cortex buffer and scrape around the outside of the craniotomy to remove any excess bone or dura.

While keeping a constant flow of cortex buffer use the aspirator to slowly remove the cortex above the hippocampus. Continue removing cortex until you reach the white striations of the corpus callosum. Very slowly and carefully remove the horizontal white striations of the corpus callosum until you reach the striations that go vertical. When you reach these striations, stop aspirating and clean up the sides so that the lens can be placed into the brain. Continue washing with cortex buffer until all bleeding stops and keep the brain constantly flushed with cortex buffer.

=== Lens implantation ===
Attach GRIN lens to lens holder on stereotax. Align the lens with the top of the skull at the most posterior part of the craniotomy and quickly insert the lens 1.35 mm below the top of the skull. Remove any excess liquid with the aspirator. Connect the outside of the GRIN lens with the skull and skull screw using cyanoacrylate glue and let fully dry or use a glue accelerator. Remove the lens holder by simply removing the vacuum suction (you can just pinch the tubing) and withdrawing the holder. Next, cover the entire skull with cyanoacrylate glue, and then cover with dental cement. Let dry completely and cover with Kwik-Sil to protect the lens. Remove from stereotax and allow the animal to recover. Give the animal amoxicillin (or equivalent) for 7 days, and daily injections of carprofen and dexamethasone for 7 days.

=== Important tips to remember ===
*Try to keep the surgery as sterile as possible. Infections will destroy imaging and the ability to keep the same cells over many days.

*Try to keep isoflurane as low as possible. Surgeries can take 2-6 hours depending on experience.

*Aspirations will take a lot of practice. Go slow at first.

*Depth will be trial and error. If the first few animals don't give good images, check the depth using histology and adjust accordingly.

Please feel free to add any tips that you have!

== Baseplating Protocol ==

Surgery Protocol

2016-03-25T18:58:55Z

Tristanshuman:

The following is a basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging. For videos of surgery and baseplating, see the [Online Workshop].

In order to image, animals will need to undergo three surgical procedures: a virus injection, a GRIN lens implantation, and baseplate attachment.

== Virus Injection ==
Before implanting the GRIN lens, you will need to inject a fluorescent indicator such as GCaMP6. We have generally used AAV1.Syn.GCaMP6f.WPRE.SV40 from Penn Vector (Item number AV-1-PV2822) and had great success in dorsal CA1. You may also be able to use GCaMP6 transgenic mice, but we have not tested whether any of the newer lines are bright enough to be imaged.

== GRIN Lens Implantation==

=== Basic Equipment Needed ===
You will only need basic surgical equipment to perform GRIN lens implantation surgeries. This includes a mouse stereotax, an isoflurane vaporizor, surgical heat pad, stereo surgical microscope, light source, dental drill, and bead sterilizer. For recommended equipment, see the master [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].

You will need the following basic tools and supplies: fine forceps, blunt forceps, fine scissors, scalpel and blade, small skull screws, drill bits, cyanoacrylate glue, dental cement, Kwik-Sil, and [[cortex buffer]]

=== Aspirator and Lens Holder ===
You will need an aspirator to remove cortex above the hippocampus. This can be build very simply with a vacuum line (or pump), a liquid trap, 1 ml syringe (with a hole to control suction), blunt needles, tubing and connectors, and hot glue.
[[File:Aspirator.PNG|center|500px]]

You can easily build a GRIN lens holder by using a suction system to hold the lens in place as it is dropped into the brain for implantation. To build, start with two 1ml micropipette tips. Cut the first so that the tip is just larger than the diameter of the GRIN lens you will be using. Cut the second tip so that the end is just smaller than the size of the GRIN lens. Connect this end to a 1ml syringe and connect to a vacuum line. This will then hold the lens in place during implantation. You can then use tape to attach this holder to a stereotax. Another solution we have used is a basic drill chuck, but this is only good for large (2mm) lenses.
[[File:LensHolder.PNG|center|500px]]

=== Skull Preparation ===
You must first prepare the skull for implantation. We recommend shaving the head area and sterilizing with 3 alternating betadine and ethanol scrubs. Next, remove the scalp with scissors and clean the skull with hydrogen peroxide and saline. Scrape and score the skull to increase the bond with the glue. We also detach the neck muscle from the skull in order to reduce pull on the skull and prevent muscle growth that can make the implant less stable. Finally we insert a skull screw on the opposite side of the skull to enhance the stability of the implant.

=== Craniotomy and Aspiration ===
Using a stereotax, align the skull and find the location for the implant. Using a drill, make 4 guide holes to outline the lens placement. For CA1, we recommend offsetting the lens 0.5mm to the medial side of the virus injection to prevent imaging any damage induced by the virus injection. Connect the guide holes to create a circular craniotomy and peel off the circular skull fragment. Do not worry about blood as the top layers of cortex will be removed by aspiration. Make absolutely sure that the craniotomy is at least the size of your GRIN lens! Cover with cortex buffer and scrape around the outside of the craniotomy to remove any excess bone or dura.

While keeping a constant flow of cortex buffer use the aspirator to slowly remove the cortex above the hippocampus. Continue removing cortex until you reach the white striations of the corpus callosum. Very slowly and carefully remove the horizontal white striations of the corpus callosum until you reach the striations that go vertical. When you reach these striations, stop aspirating and clean up the sides so that the lens can be placed into the brain. Continue washing with cortex buffer until all bleeding stops and keep the brain constantly flushed with cortex buffer.

=== Lens implantation ===
Attach GRIN lens to lens holder on stereotax. Align the lens with the top of the skull at the most posterior part of the craniotomy and quickly insert the lens 1.35 mm below the top of the skull. Remove any excess liquid with the aspirator. Connect the outside of the GRIN lens with the skull and skull screw using cyanoacrylate glue and let fully dry or use a glue accelerator. Remove the lens holder by simply removing the vacuum suction (you can just pinch the tubing) and withdrawing the holder. Next, cover the entire skull with cyanoacrylate glue, and then cover with dental cement. Let dry completely and cover with Kwik-Sil to protect the lens. Remove from stereotax and allow the animal to recover. Give the animal amoxicillin (or equivalent) for 7 days, and daily injections of carprofen and dexamethasone for 7 days.

=== Important tips to remember ===
*Try to keep the surgery as sterile as possible. Infections will destroy imaging and the ability to keep the same cells over many days.

*Try to keep isoflurane as low as possible. Surgeries can take 2-6 hours depending on experience.

*Aspirations will take a lot of practice. Go slow at first.

*Depth will be trial and error. If the first few animals don't give good images, check the depth using histology and adjust accordingly.

Please feel free to add any tips that you have!

== Baseplating Protocol ==

Surgery Protocol

2016-03-25T18:58:37Z

Tristanshuman:

The following is a basic outline of our procedure for implanting a GRIN lens above the hippocampus for CA1 imaging. For videos of surgery and baseplating, see the [Workshop Resource].

In order to image, animals will need to undergo three surgical procedures: a virus injection, a GRIN lens implantation, and baseplate attachment.

== Virus Injection ==
Before implanting the GRIN lens, you will need to inject a fluorescent indicator such as GCaMP6. We have generally used AAV1.Syn.GCaMP6f.WPRE.SV40 from Penn Vector (Item number AV-1-PV2822) and had great success in dorsal CA1. You may also be able to use GCaMP6 transgenic mice, but we have not tested whether any of the newer lines are bright enough to be imaged.

== GRIN Lens Implantation==

=== Basic Equipment Needed ===
You will only need basic surgical equipment to perform GRIN lens implantation surgeries. This includes a mouse stereotax, an isoflurane vaporizor, surgical heat pad, stereo surgical microscope, light source, dental drill, and bead sterilizer. For recommended equipment, see the master [https://docs.google.com/spreadsheets/d/12H71DU2QX8d7efUE4yNuikBEiIzKaXjYqdc0A-oLNSw/edit?usp=sharing parts list].

You will need the following basic tools and supplies: fine forceps, blunt forceps, fine scissors, scalpel and blade, small skull screws, drill bits, cyanoacrylate glue, dental cement, Kwik-Sil, and [[cortex buffer]]

=== Aspirator and Lens Holder ===
You will need an aspirator to remove cortex above the hippocampus. This can be build very simply with a vacuum line (or pump), a liquid trap, 1 ml syringe (with a hole to control suction), blunt needles, tubing and connectors, and hot glue.
[[File:Aspirator.PNG|center|500px]]

You can easily build a GRIN lens holder by using a suction system to hold the lens in place as it is dropped into the brain for implantation. To build, start with two 1ml micropipette tips. Cut the first so that the tip is just larger than the diameter of the GRIN lens you will be using. Cut the second tip so that the end is just smaller than the size of the GRIN lens. Connect this end to a 1ml syringe and connect to a vacuum line. This will then hold the lens in place during implantation. You can then use tape to attach this holder to a stereotax. Another solution we have used is a basic drill chuck, but this is only good for large (2mm) lenses.
[[File:LensHolder.PNG|center|500px]]

=== Skull Preparation ===
You must first prepare the skull for implantation. We recommend shaving the head area and sterilizing with 3 alternating betadine and ethanol scrubs. Next, remove the scalp with scissors and clean the skull with hydrogen peroxide and saline. Scrape and score the skull to increase the bond with the glue. We also detach the neck muscle from the skull in order to reduce pull on the skull and prevent muscle growth that can make the implant less stable. Finally we insert a skull screw on the opposite side of the skull to enhance the stability of the implant.

=== Craniotomy and Aspiration ===
Using a stereotax, align the skull and find the location for the implant. Using a drill, make 4 guide holes to outline the lens placement. For CA1, we recommend offsetting the lens 0.5mm to the medial side of the virus injection to prevent imaging any damage induced by the virus injection. Connect the guide holes to create a circular craniotomy and peel off the circular skull fragment. Do not worry about blood as the top layers of cortex will be removed by aspiration. Make absolutely sure that the craniotomy is at least the size of your GRIN lens! Cover with cortex buffer and scrape around the outside of the craniotomy to remove any excess bone or dura.

While keeping a constant flow of cortex buffer use the aspirator to slowly remove the cortex above the hippocampus. Continue removing cortex until you reach the white striations of the corpus callosum. Very slowly and carefully remove the horizontal white striations of the corpus callosum until you reach the striations that go vertical. When you reach these striations, stop aspirating and clean up the sides so that the lens can be placed into the brain. Continue washing with cortex buffer until all bleeding stops and keep the brain constantly flushed with cortex buffer.

=== Lens implantation ===
Attach GRIN lens to lens holder on stereotax. Align the lens with the top of the skull at the most posterior part of the craniotomy and quickly insert the lens 1.35 mm below the top of the skull. Remove any excess liquid with the aspirator. Connect the outside of the GRIN lens with the skull and skull screw using cyanoacrylate glue and let fully dry or use a glue accelerator. Remove the lens holder by simply removing the vacuum suction (you can just pinch the tubing) and withdrawing the holder. Next, cover the entire skull with cyanoacrylate glue, and then cover with dental cement. Let dry completely and cover with Kwik-Sil to protect the lens. Remove from stereotax and allow the animal to recover. Give the animal amoxicillin (or equivalent) for 7 days, and daily injections of carprofen and dexamethasone for 7 days.

=== Important tips to remember ===
*Try to keep the surgery as sterile as possible. Infections will destroy imaging and the ability to keep the same cells over many days.

*Try to keep isoflurane as low as possible. Surgeries can take 2-6 hours depending on experience.

*Aspirations will take a lot of practice. Go slow at first.

*Depth will be trial and error. If the first few animals don't give good images, check the depth using histology and adjust accordingly.

Please feel free to add any tips that you have!

== Baseplating Protocol ==

User:Tristanshuman

2016-03-21T19:18:48Z

Tristanshuman:

Tristan Shuman, PhD 
Golshani Lab, UCLA 
tristanshuman@gmail.com

I'm a postdoc in Peyman Golshani's lab working on the circuit reorganization induced by chronic seizures, and how we can rescue seizures and cognitive deficits with interneuron transplantation in chronically epileptic mice.

User:Tristanshuman

2016-03-21T19:18:24Z

Tristanshuman:

Tristan Shuman, PhD 
Golshani Lab
UCLA
tristanshuman@gmail.com

I'm a postdoc in Peyman Golshani's lab working on the circuit reorganization induced by chronic seizures, and how we can rescue seizures and cognitive deficits with interneuron transplantation in chronically epileptic mice.