Difference between revisions of "Other Open Source Projects"
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Listed below are open-source projects being tackled by other groups. | Listed below are open-source projects being tackled by other groups. | ||
| + | |||
| + | == Recommended Analysis Packages == | ||
| + | We currently recommend using the following combination of packages for Miniscope analysis | ||
| + | *Image Registration: [https://github.com/flatironinstitute/NoRMCorre NoRMCorre] or [https://scanbox.wordpress.com/2014/03/20/recursive-image-alignment-and-statistics/ Dario Ringach's recursive image registration algorithm]. NoRMCorre can correct for both local and global rigid motion while Dario's approach works just on a global level. | ||
| + | *Neuron segmentation and activity extraction: [https://github.com/zhoupc/CNMF_E CNMF-E] works extremely well for Miniscope imaging. It can denoise, demix, and deconvolve neural activity. | ||
| + | *Tracking neurons across days: [https://github.com/zivlab/CellReg CellReg] | ||
| + | |||
| + | 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 [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." | ||
| + | |||
| + | A new approach, as of June 2018, has come out for analyzing 1 photon imaging data. While we haven't tested this pipeline ourselves yet, it looks extremely promising. | ||
| + | *[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]. | ||
| + | |||
| + | == 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]] | ||
| + | |||
| + | == 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] | ||
| + | |||
| + | == PoMiDAQ - Portable Miniscope Data Acquisition Software == | ||
| + | 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/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 == | == Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN == | ||
| − | Description, pictures, drawings and part files for a Miniscope baseplate and protective cone. | + | Description, pictures, drawings, and part files for a Miniscope baseplate and protective cone. |
[[Miniscope Baseplate and Protective Cone for Rats]] | [[Miniscope Baseplate and Protective Cone for Rats]] | ||
| + | |||
| + | == Miniscope Gripper by Bastijn van den Boom at NIN == | ||
| + | Description, pictures, drawings, and part files for a Miniscope gripper for holding the Miniscope while baseplating. | ||
| + | |||
| + | [[Miniscope Gripper]] | ||
== Miniscope Bonsai Package by Jon Newman == | == Miniscope Bonsai Package by Jon Newman == | ||
| Line 15: | Line 51: | ||
[[CNMF-E]] | [[CNMF-E]] | ||
| − | https://github.com/zhoupc/CNMF_E | + | https://github.com/zhoupc/CNMF_E (Matlab) |
== Miniature Microscope from the Gardner Lab at Boston University == | == Miniature Microscope from the Gardner Lab at Boston University == | ||
Latest revision as of 06:57, 18 June 2019
Listed below are open-source projects being tackled by other groups.
Contents
- 1 Recommended Analysis Packages
- 2 OvalDrive 18-ES
- 3 ONE Core Miniscope Modifications
- 4 PoMiDAQ - Portable Miniscope Data Acquisition Software
- 5 Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN
- 6 Miniscope Gripper by Bastijn van den Boom at NIN
- 7 Miniscope Bonsai Package by Jon Newman
- 8 Constrained Nonnegative Matrix Factorization for microEndoscopic data
- 9 Miniature Microscope from the Gardner Lab at Boston University
- 10 Open-Ephys
- 11 OpenMaze
- 12 Open Behavior
Recommended Analysis Packages
We currently recommend using the following combination of packages for Miniscope analysis
- Image Registration: NoRMCorre or Dario Ringach's recursive image registration algorithm. NoRMCorre can correct for both local and global rigid motion while Dario's approach works just on a global level.
- Neuron segmentation and activity extraction: CNMF-E works extremely well for Miniscope imaging. It can denoise, demix, and deconvolve neural activity.
- Tracking neurons across days: CellReg
Luckily, multiple groups are working on analysis packages which combine the approaches listed above into a single workflow:
- 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.
- 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.
- 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."
A new approach, as of June 2018, has come out for analyzing 1 photon imaging data. While we haven't tested this pipeline ourselves yet, it looks extremely promising.
- 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 here.
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
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: ONE Core Miniscope Page
PoMiDAQ - Portable Miniscope Data Acquisition Software
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 source code on GitHub or download a binary build for Windows or Linux.
Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN
Description, pictures, drawings, and part files for a Miniscope baseplate and protective cone.
Miniscope Baseplate and Protective Cone for Rats
Miniscope Gripper by Bastijn van den Boom at NIN
Description, pictures, drawings, and part files for a Miniscope gripper for holding the Miniscope while baseplating.
Miniscope Bonsai Package by Jon Newman
"Bonsai package for controlling and acquiring data from headborne miniscopes for calcium imaging"
Constrained Nonnegative Matrix Factorization for microEndoscopic data
Analysis package for (1) identifying spatial footprints of all neurons and (2) denoising, demixing and deconvolving the temporal signals.
CNMF-E https://github.com/zhoupc/CNMF_E (Matlab)
Miniature Microscope from the Gardner Lab at Boston University
Gardner Lab Miniature Microscope
Open-Ephys
"A team of neuroscientists who want to change the way our tools are developed and shared."
OpenMaze
"Open source hardware and software for behavioral neuroscience. Learn how to design and build fully functional animal behavioral setups rapidly, cheaply, and easily."
Open Behavior
"Open Behavior is dedicated to accelerating behavioral neuroscience research through the promotion of collaboration and open-source projects."
