UCLA Miniscope - User contributions [en]

Contributors

2020-07-31T22:40:08Z

Myqlavu:

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, Department of Neurology at the David Geffen School of Medicine, 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

;Mimi La-Vu
:Research Associate, Silva Lab, UCLA
:myqlavu@ucla.edu

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

Initial Testing of Assembled Miniscopes

2017-10-11T20:43:14Z

Myqlavu: /* Testing the Stability of the DAQ Software */

'''This page is a work in progress.'''

Once your Miniscope system is up and running, it is important to be able to test, and debug, all aspects of the system before moving to imaging in vivo. The sections below will discuss the procedures we use to validate Miniscopes we build before using them in experiments. As you become more comfortable with using Miniscopes some of the sections below can be skipped.

== Testing the Coaxial Cable Connection ==
In our experience, the connection of the coax cable, either to the CMOS Imaging Sensor PCB or SMA connector, is by far the most common point of failure when building a Miniscope System. Take care when soldering these connections not to short the inner conductor to the outer shield. It helps to cover the solder joint as well as ~1cm of coax cable extending from the solder join in a semi-flexible epoxy, silicone, or glue (hot glue works well) to take the strain of cable movement off of the solder joint.

Once assembled, connect the Miniscope system to your computer and run the DAQ software. With the video streaming from the scope, move/twist/wiggle the coax cable with greater intensity that what you would expect an animal to apply, especially at the ends of the cable. If soldered correctly, the video stream should not drop out even with excessive movement and twisting of the cable.

== Testing the Stability of the DAQ Software ==
[[File:SoftwareTests.png|right|500px]]
When running your Miniscope system on a new computer it is important to check the following
*'''Stability of video stream:''' We have found some combinations of USB drivers, computer hardware, and Window's OS can lead to the video stream failing a few minutes after the software has connected to the scope. This seems to mainly be an issue with Windows 8 and is independent of if you are recording the video to disk. To test the stability of your system,
*#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
*#Open up the DAQ software and connect to the Miniscope.
*#Leave the system running for 5 minutes. Do not click the 'record' button.
*#If the video stream is still present (not Red Screen of Doom) your system should not have any driver or OS issues.
*'''Streaming video frame rate:''' The default frame rate of your Miniscope system is 30FPS but can be adjusted using the drop down 'Frame Rate' box in our DAQ software (labeled with a red '1' in the picture to the right).
*#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
*#Open up the DAQ software and connect to the Miniscope.
*#Observe the current frame rate (labeled with a red '2' in the picture to the right). It should be stable within 1 FPS from the expected value. This is just an approximate measure of the frame rate, the frame rate of the recorded video should be extremely stable.
*#You can also connect to a behavioral camera to add strain on your system. Generally the behavioral camera will have larger fluctuations in the displayed frame rate.
*'''Write speed of video data:''' You want to make sure your computer is able to write the uncompressed video data to your HDD or SSD as quick (and hopefully much quicker than) as the rate at which you are acquiring it. Slow or encryted hard drives can be a source of problems here.
*#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
*#Open up the DAQ software and connect to the Miniscope.
*#Click 'record' and observe the 'Write Speed (fps)' (labled with a red '3' in the picture to the right). This box displays the current write speed of your data. The number displayed will fluctuate but should stay above the acquisition frame rate of your Miniscope. If the write speed falls below the acquisition frame rate, video frames will be written into a circular buffer which is 256 frames long. If the write speed stays low for too long the software will begin to overwrite frames in the circular buffer. The 'timestamps.dat' file created during recording keeps track of the buffer size and is an addition place you can look when evaluating the write speed of your computer.
 

== Imaging Your Surroundings ==
[[File:ImagingWithoutGRINLens.png|right|500px]]
An assembled scope can image your surrounds when a GRIN lens is '''not placed''' into the hole in the base of the scope. Connect the scope to your computer and then point the base of the scope toward objects that are illuminated with room or sun light.
*The scope has a green bandpass filter sitting before the CMOS imaging sensor. This means you will only be collecting light between 500nm and 550nm.
*Most objects in the environment will not fluoresce under the blue excitation LED. This means most object will not show up unless being illuminated by a light source that contains green wavelengths such as room light or sunlight.
*Adjust the focus slider to adjust the focal plane of your Miniscope. Most object will appear to be "infinitely" far away from the CMOS imaging sensor. Your focus slider will need to be placed close to its highest point in order to focus on these objects. This focusing slider position is equivalent to imaging at the bottom surface of your GRIN lens if a GRIN lens was mounted into the base of the scope.

 

== Checking for Light Leakage ==
[[File:LightLeakage.png|right|500px]]
When assembled correctly, no excitation light from the LED should leak onto the CMOS imaging sensor in your scope. The following steps will walk you through testing a scope for such light leakage. If you do find that your scope leaks light the most common sources of the leak are the excitation or emission filter being scratched, placed in the wrong orientation, or significantly misaligned.
#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
#Open up the DAQ software and connect to the Miniscope.
#Place the opening in the base of the scope (you can do this with or without a GRIN lens) against a black surface that won't fluoresce. You may be surprised at what materials weakly fluoresce green when blasted with blue excitation light.
#Turn the exposure and gain of the scope to their maximum values.
#Slowly turn up the excitation LED power from 0% to max power. Depending on your scope and DAQ software version the LED will likely max out at around 40%.
#As you increase the LED power watch the video stream for large increases in pixel brightness across large regions of your image. A small overall increase in pixel value of ~20 (the pixel values range from 0 to 255) is expected. You may also notice at max gain that some pixels become noisy. This is also normal but care should be taken in experiments to minimize this noise by limiting the gain or by correct these noisy pixels during offline processing of your data.

 

== Imaging Calibration Slides ==
[[File:ImagingTestSlide.png|right|500px]]
[[File:MiniscopeCalibrationSlide.png|thumb|right|500px|Image of a calibration slide with 9.8μm line spacing (superimposed red boxes are 10px x 10px)]]

This is probably the most important initial test you can do with your Miniscope system. Not only can it uncover issues in your system but will also give you a good sense of how the optics, imaging, and focusing slider work. The figure to the right shows a modified test/calibration slide (left), optional GRIN lens holder (middle), and example configuration for imaging a test slide (right).
*The modified test/calibration slide is a [http://www.thorlabs.us/navigation.cfm?guide_id=2332 resolution test slide] with [http://www.amazon.com/JVCC-Stage-Set-Spike-Tape-Fluorescent/dp/B000QDVNH0/ref=sr_1_12?s=industrial&srs=2529683011&ie=UTF8&qid=1461180753&sr=1-12 green fluorescing tape] attached to the underside of the glass. It is important that the printed surface of the test slide be the side that is closest to the GRIN lens. Different thicknesses of cover glass can be used between the test slide and GRIN lens to get a feeling for imaging at different depths.
*The middle picture shows a simple GRIN lens holder we had made. This holder is a block of Delrin plastic with different diameter holes drilled into it. a GRIN lens can be placed into the holder and then set on top of the modified test slide. A Miniscope can then be set onto of the holder to image the slide. The holder does a nice job keeping the surface of the GRIN lens co-planer to the surface of the test slide.
*The right picture should an example configuration to image a test slide. This picture is of a scope that has been modified, [Imaging With Thin GRIN Lenses], to hold a GRIN lens in its base. While the picture shows the scope being held by hand, one could easily mount the scope in a clamp for more stable imaging. If using a GRIN lens holder as described above, a similar configuration would be used except the GRIN lens and holder would be in place of the bare GRIN lens.

The image on the bottom right is of a calibration slide with 9.8μm line spacing (superimposed red boxes are 10px x 10px).
 

== Imaging GFP Slides ==
{{#ev:youtube|https://youtu.be/lxEUkP-YI8g|640|right}}
Similar to imaging test slides, you can use your Miniscope to image brain slice slides expressing GFP or slides with other fluorescent sources. A few key points for imaging slides are listed below:
*Your scope has a green bandpass filter (500nm to 550nm) in front the the CMOS imaging sensor. This means you will only be able to see green fluorescence.
*Take note of the thickness of your cover slip, usually around 170um thick. You will be imaging through the cover slip to reach the fluorescing sample. If you are using less than a 15mm focal length achromatic lens, you will likely not be able to focus past the bottom of the cover slip. Even a 15mm focal length achromatic lens will generally just reach about 50um below the bottom of the cover slip with the focusing slider pushed to its lowest position.

The video to the right is of a TetTag GFP slide being imaged with a 15mm focal length achromatic lens and 0.25 pitch GRIN lens. A few notes:
*There are some compression artifacts present due to YouTube's compression of the video.
*The disk of light near the center of the field of view is due to reflection of the fluorescent light between the cover slip and bottom of GRIN lens... you should not see this disk when imaging in vivo.
*The left and right portions of the field of view are dimmer than what you should expect to see with your own system. The outer dimness was greatly reduced in the newer versions of the Miniscope main body.

System Assembly

2017-10-11T19:02:33Z

Myqlavu: /* Soldering SMA Connector to Coaxial Cable */

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 is 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]]

Initial Testing of Assembled Miniscopes

2017-10-11T18:19:47Z

Myqlavu: /* Imaging GFP Slides */

'''This page is a work in progress.'''

Once your Miniscope system is up and running, it is important to be able to test, and debug, all aspects of the system before moving to imaging in vivo. The sections below will discuss the procedures we use to validate Miniscopes we build before using them in experiments. As you become more comfortable with using Miniscopes some of the sections below can be skipped.

== Testing the Coaxial Cable Connection ==
In our experience, the connection of the coax cable, either to the CMOS Imaging Sensor PCB or SMA connector, is by far the most common point of failure when building a Miniscope System. Take care when soldering these connections not to short the inner conductor to the outer shield. It helps to cover the solder joint as well as ~1cm of coax cable extending from the solder join in a semi-flexible epoxy, silicone, or glue (hot glue works well) to take the strain of cable movement off of the solder joint.

Once assembled, connect the Miniscope system to your computer and run the DAQ software. With the video streaming from the scope, move/twist/wiggle the coax cable with greater intensity that what you would expect an animal to apply, especially at the ends of the cable. If soldered correctly, the video stream should not drop out even with excessive movement and twisting of the cable.

== Testing the Stability of the DAQ Software ==
[[File:SoftwareTests.png|right|500px]]
When running your Miniscope system on a new computer it is important to check the following
*'''Stability of video stream:''' We have found some combinations of USB drivers, computer hardware, and Window's OS can lead to the video stream failing a few minutes after the software has connected to the scope. This seems to mainly be an issue with Windows 8 and is independent of if you are recording the video to disk. To test the stability of your system,
*#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
*#Open up the DAQ software and connect to the Miniscope.
*#Leave the system running for 5 minutes. Do not click the 'record' button.
*#If the video stream is still present (not Red Screen of Doom) your system should not have any driver or OS issues.
*'''Streaming video frame rate:''' The default frame rate of your Miniscope system is 30FPS but can be adjusted using the drop down 'Frame Rate' box in our DAQ software (labeled with a red '1' in the picture to the right).
*#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
*#Open up the DAQ software and connect to the Miniscope.
*#Observe the current frame rate (labeled with a red '2' in the picture to the right). It should be stable within 1 FPS from the expected value. This is just an approximate measure of the frame rate, the frame rate of the recorded video should be extremely stable.
*#You can also connect to a behavioral camera to add strain on your system. Generally the behavioral camera will have larger fluctuations in the displayed frame rate.
*'''Write speed of video data:''' You want to make sure your computer is able to write the uncompressed video data to your HDD or SSD as quick (and hopefully much quicker)than the rate at which you are acquiring it. Slow or encryted hard drives can be a source of problems here.
*#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
*#Open up the DAQ software and connect to the Miniscope.
*#Click 'record' and observe the 'Write Speed (fps)' (labled with a red '3' in the picture to the right). This box displays the current write speed of your data. The number displayed will fluctuate but should stay above the acquisition frame rate of your Miniscope. If the write speed falls below the acquisition frame rate, video frames will be written into a circular buffer which is 256 frames long. If the write speed stays low for too long the software will begin to overwrite frames in the circular buffer. The 'timestamps.dat' file created during recording keeps track of the buffer size and is an addition place you can look when evaluating the write speed of your computer.
 

== Imaging Your Surroundings ==
[[File:ImagingWithoutGRINLens.png|right|500px]]
An assembled scope can image your surrounds when a GRIN lens is '''not placed''' into the hole in the base of the scope. Connect the scope to your computer and then point the base of the scope toward objects that are illuminated with room or sun light.
*The scope has a green bandpass filter sitting before the CMOS imaging sensor. This means you will only be collecting light between 500nm and 550nm.
*Most objects in the environment will not fluoresce under the blue excitation LED. This means most object will not show up unless being illuminated by a light source that contains green wavelengths such as room light or sunlight.
*Adjust the focus slider to adjust the focal plane of your Miniscope. Most object will appear to be "infinitely" far away from the CMOS imaging sensor. Your focus slider will need to be placed close to its highest point in order to focus on these objects. This focusing slider position is equivalent to imaging at the bottom surface of your GRIN lens if a GRIN lens was mounted into the base of the scope.

 

== Checking for Light Leakage ==
[[File:LightLeakage.png|right|500px]]
When assembled correctly, no excitation light from the LED should leak onto the CMOS imaging sensor in your scope. The following steps will walk you through testing a scope for such light leakage. If you do find that your scope leaks light the most common sources of the leak are the excitation or emission filter being scratched, placed in the wrong orientation, or significantly misaligned.
#Connect a scope to the DAQ Box and then the DAQ Box to the computer.
#Open up the DAQ software and connect to the Miniscope.
#Place the opening in the base of the scope (you can do this with or without a GRIN lens) against a black surface that won't fluoresce. You may be surprised at what materials weakly fluoresce green when blasted with blue excitation light.
#Turn the exposure and gain of the scope to their maximum values.
#Slowly turn up the excitation LED power from 0% to max power. Depending on your scope and DAQ software version the LED will likely max out at around 40%.
#As you increase the LED power watch the video stream for large increases in pixel brightness across large regions of your image. A small overall increase in pixel value of ~20 (the pixel values range from 0 to 255) is expected. You may also notice at max gain that some pixels become noisy. This is also normal but care should be taken in experiments to minimize this noise by limiting the gain or by correct these noisy pixels during offline processing of your data.

 

== Imaging Calibration Slides ==
[[File:ImagingTestSlide.png|right|500px]]
[[File:MiniscopeCalibrationSlide.png|thumb|right|500px|Image of a calibration slide with 9.8μm line spacing (superimposed red boxes are 10px x 10px)]]

This is probably the most important initial test you can do with your Miniscope system. Not only can it uncover issues in your system but will also give you a good sense of how the optics, imaging, and focusing slider work. The figure to the right shows a modified test/calibration slide (left), optional GRIN lens holder (middle), and example configuration for imaging a test slide (right).
*The modified test/calibration slide is a [http://www.thorlabs.us/navigation.cfm?guide_id=2332 resolution test slide] with [http://www.amazon.com/JVCC-Stage-Set-Spike-Tape-Fluorescent/dp/B000QDVNH0/ref=sr_1_12?s=industrial&srs=2529683011&ie=UTF8&qid=1461180753&sr=1-12 green fluorescing tape] attached to the underside of the glass. It is important that the printed surface of the test slide be the side that is closest to the GRIN lens. Different thicknesses of cover glass can be used between the test slide and GRIN lens to get a feeling for imaging at different depths.
*The middle picture shows a simple GRIN lens holder we had made. This holder is a block of Delrin plastic with different diameter holes drilled into it. a GRIN lens can be placed into the holder and then set on top of the modified test slide. A Miniscope can then be set onto of the holder to image the slide. The holder does a nice job keeping the surface of the GRIN lens co-planer to the surface of the test slide.
*The right picture should an example configuration to image a test slide. This picture is of a scope that has been modified, [Imaging With Thin GRIN Lenses], to hold a GRIN lens in its base. While the picture shows the scope being held by hand, one could easily mount the scope in a clamp for more stable imaging. If using a GRIN lens holder as described above, a similar configuration would be used except the GRIN lens and holder would be in place of the bare GRIN lens.

The image on the bottom right is of a calibration slide with 9.8μm line spacing (superimposed red boxes are 10px x 10px).
 

== Imaging GFP Slides ==
{{#ev:youtube|https://youtu.be/lxEUkP-YI8g|640|right}}
Similar to imaging test slides, you can use your Miniscope to image brain slice slides expressing GFP or slides with other fluorescent sources. A few key points for imaging slides are listed below:
*Your scope has a green bandpass filter (500nm to 550nm) in front the the CMOS imaging sensor. This means you will only be able to see green fluorescence.
*Take note of the thickness of your cover slip, usually around 170um thick. You will be imaging through the cover slip to reach the fluorescing sample. If you are using less than a 15mm focal length achromatic lens, you will likely not be able to focus past the bottom of the cover slip. Even a 15mm focal length achromatic lens will generally just reach about 50um below the bottom of the cover slip with the focusing slider pushed to its lowest position.

The video to the right is of a TetTag GFP slide being imaged with a 15mm focal length achromatic lens and 0.25 pitch GRIN lens. A few notes:
*There are some compression artifacts present due to YouTube's compression of the video.
*The disk of light near the center of the field of view is due to reflection of the fluorescent light between the cover slip and bottom of GRIN lens... you should not see this disk when imaging in vivo.
*The left and right portions of the field of view are dimmer than what you should expect to see with your own system. The outer dimness was greatly reduced in the newer versions of the Miniscope main body.

Online Workshop

2016-06-14T21:54:11Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx | 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/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/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

2016-06-14T21:53:51Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx | 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/16PqPmxzj13-gSA0zPrVQqxB51RxaBzTs3DFlo_rBX6w/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

2016-06-14T21:52:32Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx | 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 ===
=== 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

2016-06-14T21:49:11Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx | 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 ===
=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===

Online Workshop

2016-06-14T21:49:00Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx| 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 ===
=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===

Online Workshop

2016-06-14T21:47:04Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx | 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 ===
=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===

Online Workshop

2016-06-14T21:46:25Z

Myqlavu: /* 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://drive.google.com/file/d/0ByUbjrn9MxK0N0h4SS1OM1VJcDA/view?usp=sharing 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://dl.dropboxusercontent.com/u/42465128/MINIscope/Data%20Acquisition%20and%20Image%20Processing%E2%80%8B%C2%AD.pptx| 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 ===
=== Image Acquisition and Lens Testing ===
=== In Vivo Imaging and Behavior===

Main Page

2016-03-19T02:12:29Z

Myqlavu: /* 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 around 3 grams and uses only a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data. The goal of this wiki site is to provide 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 technology. The initial goal is to help disseminate this technology to the larger neuroscience community so that we can build a community of users that will continue to develop this technology and share on these developments. 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 a standard 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. 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, 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]]).

== 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]]

 
== Discussion Board and FAQ ==
:[[Special:WikiForum|Discussion Board]]
:[[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]]
# [[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.

A free one-day workshop will be held at this year's Molecular Cellular Cognition Society Meeting in San Diego on November 10th. You can register for the workshop [http://www.iclm.ucla.edu/MiniscopeWorkshopMCCS.html here]. Space is limited.

<gallery widths=300px heights=200px mode="packed">
Image:Workshop_Jan2016.jpg|January 2016 Workshop
Image:Workshop_Mar2016.jpg|March 2016 Workshop
</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 ==
;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

User:MyQLaVu

2016-03-19T02:11:28Z

Myqlavu: Created page with " == Headline text == Mimi La-Vu Silva Lab myqlavu@gmail.com"

== Headline text ==
Mimi La-Vu
 Silva Lab
 myqlavu@gmail.com

Member Pages

2016-03-19T02:07:09Z

Myqlavu: /* Miniscope Team */

Below is a list of miniscope.org member created pages. These pages are a place for community members to share their contact information, current work, interests, and whatever else they find relevant. A major goal of miniscope.org is to foster an environment of open sharing, communication, and collaboration.

You can reach your own member page by clicking your account name at the top right of the page or by going to "http://miniscope.org/index.php?title=User:XXXX", replacing 'XXXX' with your user name. Member pages can be modified by that member without needing approval by an administrator. If you would like to add a link to your member page here, please do so by editing this page or posting a thread on the discussion board.

== Miniscope Team ==
{| class="wikitable"
|-
! scope="col"| Name
! scope="col"| Member Page
! scope="col"| Lab
! scope="col"| University
|-
! Daniel Aharoni
| [[User:DAharoni|DAharoni]]
| Golshani, Silva, Khakh
| UCLA
|-
! Tristan Shuman
| [[User:Tristanshuman|Tristanshuman]]
| Golshani
| UCLA
|-
! Denise Cai
| [[User:Denisecai|Denisecai]]
| Silva
| UCLA
|-
! Mimi La-Vu
| [[User:MyQLaVu|MyQLaVu]]
| Silva
| UCLA
|}

== Americas ==
{| class="wikitable"
|-
! scope="col"| Name
! scope="col"| Member Page
! scope="col"| Lab
! scope="col"| University
|}
== Europe ==
{| class="wikitable"
|-
! scope="col"| Name
! scope="col"| Member Page
! scope="col"| Lab
! scope="col"| University
|}
== Asia ==
{| class="wikitable"
|-
! scope="col"| Name
! scope="col"| Member Page
! scope="col"| Lab
! scope="col"| University
|}

System Assembly

2016-02-17T23:35:40Z

Myqlavu: /* Head Mounted Scope Assembly */

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

=== Filter Edge Blackening (Suggested) ===
While not strictly necessary, we suggest blackening the sides of the dichroic and emission filters. 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 LED to PCB ===
{{#ev:youtube|8KWx6qv82ts|640|center}}

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

=== 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 ==
We generally have all surface mount (SMD) components assembled on the DAQ PCB by a third party PCB assembly house leaving only the through-hole components to be assembled in lab. It is possible to have the assembly house place both SMD and through-hole components but it is more expensive and through-hole components are relatively easy to solder. A good through-hole soldering tutorial can be found [https://learn.sparkfun.com/tutorials/how-to-solder---through-hole-soldering here].

=== Through-hole component assembly ===
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|600px]]

*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}}

=== 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]]

== 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 carry should still be taken to minimize these loses.

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.

Main Page

2016-01-27T22:23:46Z

Myqlavu:

[[File:miniscopev2.JPG|thumb|300px]]
Welcome to Miniscope.org Wiki!

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 around 3 grams and uses only a single, flexible coaxial cable (0.3mm to 1.5mm diameter) to carry power, control signals, and imaging data. The goal of this wiki site is to provide 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 technology. The initial goal is to help disseminate this technology to the larger neuroscience community so that we can build a community of users that will continue to develop this technology and share on these developments. 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 a standard 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. 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, 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]]).

== 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]]

 
== Discussion Board and FAQ ==
:[[Special:WikiForum|Discussion Board]]
:[[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]]
# [[Surgery Protocol]]
# [[Animal Behavior Guide]]

== Update Log ==
;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