Other Open Source Projects
Listed below are open-source projects being tackled by other groups.
Contents
- 1 Recommended Analysis Packages
- 2 Miniscope Baseplate and Protective Cone for Rats by Bastijn van den Boom at NIN
- 3 Miniscope Gripper by Bastijn van den Boom at NIN
- 4 Miniscope Bonsai Package by Jon Newman
- 5 Constrained Nonnegative Matrix Factorization for microEndoscopic data
- 6 Miniature Microscope from the Gardner Lab at Boston University
- 7 Open-Ephys
- 8 OpenMaze
- 9 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."
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."
