Other Open Source Projects - Revision history

MatthiasK at 11:57, 18 June 2019

2019-06-18T11:57:24Z

2019-05-30T11:52:33Z

Add PoMiDAQ

2018-10-31T16:58:28Z

‎OvalDrive 18-ES

2018-10-31T16:58:19Z

2018-06-21T17:10:22Z

‎Recommended Analysis Packages

2018-05-24T16:17:37Z

‎ONE Core Miniscope Modifications

2018-05-24T16:17:15Z

2018-05-10T20:34:40Z

‎Recommended Analysis Packages

2018-05-10T20:33:41Z

‎Recommended Analysis Packages

2018-05-09T22:00:41Z

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 This software can be used instead of the existing Miniscope DAQ Software. It features (lossless and fast) FFV1 encoding of the recorded video by default, as well as a feature to do online background subtraction. The software runs on Windows and Linux.
-Check out the [https://github.com/ximion/pomidaq source code on GitHub] or [https://github.com/ximion/pomidaq/releases download a binary build for Windows or Linux].
+Check out the [https://github.com/bothlab/pomidaq source code on GitHub] or [https://github.com/bothlab/pomidaq/releases download a binary build for Windows or Linux].
 == Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN ==

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 Check it out here:
 [https://optogeneticsandneuralengineeringcore.github.io/ONECoreSite/projects/Miniscope/ ONE Core Miniscope Page]
 == Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN ==

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 == OvalDrive 18-ES ==
 Developed by the Blair Lab at UCLA, up to 18 individually movable probes can be implanted alongside the UCLA miniscope for simultaneous electrophysiological recording and calcium imaging in rats.
 Check it out here: [[OvalDrive36 and OvalDrive18-ES]]

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 *[https://github.com/JinghaoLu/MIN1PIPE MIN1PIPE]: "MIN1PIPE is a fully automatic, Matlab-based toolbox, solving the full range problems in 1-photon calcium imaging in one package: data enhancement → movement morrection → signal extraction. It requires minimal parameter-tuning and integrates the semi-auto options. Each inidividual module can also be easily adapted for the 2-photon imaging setting."
 * Associated paper can be found [https://www.biorxiv.org/content/early/2018/04/30/311548 here].
 == ONE Core Miniscope Modifications ==

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 *[https://github.com/PeyracheLab/miniscoPy MiniscoPy]: "A [Python] package to analyse calcium imaging data recorded with the Miniscope." This package is being developed by Adrien Peyrache's lab at McGill and is based on the CaImAn toolbox.
 *[https://github.com/etterguillaume/MiniscopeAnalysis MiniscopeAnalysis]:"Analysis package for miniscope data Written by Guillaume Etter (Sylvain Williams Lab, McGill University) This is an updated version of the Miniscope analysis package developed by Daniel Aharoni at UCLA in collaboration with the Golshani lab, Silva lab, and Khaki lab. It combines core functions of the original ms analysis package with NormCorre alignment and CNMFE source extraction."
 == ONE Core Miniscope Modifications ==

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 == ONE Core Miniscope Modifications ==
-This is work done by Andrew Scallon at the Optogenetics and Neural Engineering (ONE) Core at the University of Colorado, Denver School of Medicine. They have designs and descriptions for a new DAQ Box, Miniscope holder, and Miniscope body all optimized for 3D printing! Check it out here: [https://optogeneticsandneuralengineeringcore.github.io/ONECoreSite/projects/Miniscope/ ONE Core Miniscope Page]
+This is work done by Andrew Scallon at the Optogenetics and Neural Engineering (ONE) Core at the University of Colorado, Denver School of Medicine. They have designs and descriptions for a new DAQ Box, Miniscope holder, and Miniscope body all optimized for 3D printing!
 == Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN ==

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 Luckily, multiple groups are working on analysis packages which combine the approaches listed above into a single workflow:
 *[https://github.com/flatironinstitute/CaImAn CaImAn]: "Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization." This toolbox is very well maintained by the Simons Foundation and generally has the most up-to-date versions of NoRMCorre and CNMF.
-*[https://github.com/PeyracheLab/miniscoPy MiniscoPy]: "A package to analyse calcium imaging data recorded with the Miniscope." This package is being developed by Adrien Peyrache's lab at McGill and is based on the CaImAn toolbox.
+*[https://github.com/PeyracheLab/miniscoPy MiniscoPy]: "A [Python] package to analyse calcium imaging data recorded with the Miniscope." This package is being developed by Adrien Peyrache's lab at McGill and is based on the CaImAn toolbox.
 == Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN ==

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 Listed below are open-source projects being tackled by other groups.
 == Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN ==
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 [[CNMF-E]]
 https://github.com/zhoupc/CNMF_E  (Matlab)
 == Miniature Microscope from the Gardner Lab at Boston University ==