GitHub - mitlabence/2p-py: Python scripts for analyzing 2photon imaging data.

2p-py Installation:

Install anaconda.
Create an environment (mamba is difficult or impossible to install without an environment) with arbitrary name [env-name]. Then use conda activate [env-name] to activate it.
Install mamba in the environment with conda install -c conda-forge mamba
Install CaImAN. https://github.com/flatironinstitute/CaImAn This will create an environment inside [env-name] with mamba: mamba create -n caiman -c conda-forge caiman
conda activate caiman when in the environment [env-name].
Check python version by starting python (command: "python"). The version is most important for the Matlab Engine (running matlab code in python), see https://de.mathworks.com/help/matlab/matlab-engine-for-python.html Versions of python compatible with matlab by release.
Install opencv (cv2) python package when inside the [env-name] or caiman environment: pip install opencv-python (Windows; dirty solution, but conda installation is difficult as always)
Enter 2p-py directory and make sure caiman environment is active.
Downgrade jinja2 to 3.0.3 (2022.03.28: 3.1.1 is the current version). The reason is that "from jinja2 import Markup" had been deprecated for a long time, and was removed recently. Now the solution would be to import from markupsafe directly, which is not implemented in caiman, and the environment does not fix the jinja2 version...
while caiman env is active: pip install pims_nd2
jupyter-notebook

New way (once anaconda is installed):

To create an environment named env-name, enter the 2p-py folder and run conda create --name env-name --file 2p-py-env.txt
Proceed to manually install the missing package, as described in manually installed packages.txt.

Name		Name	Last commit message	Last commit date
Latest commit History 428 Commits
.github/workflows		.github/workflows
.idea		.idea
conda		conda
labrotation		labrotation
libs		libs
tests		tests
.env-sample		.env-sample
.gitignore		.gitignore
1a Pure Python Pipeline Splitting.ipynb		1a Pure Python Pipeline Splitting.ipynb
1b Pure Python Pipeline.ipynb		1b Pure Python Pipeline.ipynb
1c Pure Python Pipeline on Parts of Recording.ipynb		1c Pure Python Pipeline on Parts of Recording.ipynb
2 Get complete traces.ipynb		2 Get complete traces.ipynb
3a Extract neuron onset times and grid data.ipynb		3a Extract neuron onset times and grid data.ipynb
3b Review onset and grid data.ipynb		3b Review onset and grid data.ipynb
4 Directionality analysis.ipynb		4 Directionality analysis.ipynb
4b Speed analysis.ipynb		4b Speed analysis.ipynb
Add or fill UUID column to sessions.ipynb		Add or fill UUID column to sessions.ipynb
Analysis steps.txt		Analysis steps.txt
Analyze Nikon imaging parameters.ipynb		Analyze Nikon imaging parameters.ipynb
Assemble Nikon traces for baseline recovery.ipynb		Assemble Nikon traces for baseline recovery.ipynb
Assemble baseline - seizure - aftermath traces.ipynb		Assemble baseline - seizure - aftermath traces.ipynb
Assemble bilateral stim traces.ipynb		Assemble bilateral stim traces.ipynb
Assemble traces for ChR2 stim protocol.ipynb		Assemble traces for ChR2 stim protocol.ipynb
Baseline recovery 2.0.ipynb		Baseline recovery 2.0.ipynb
Baseline recovery.ipynb		Baseline recovery.ipynb
Bulk extract TwoPhotonSession.ipynb		Bulk extract TwoPhotonSession.ipynb
Caiman + matching pipeline.ipynb		Caiman + matching pipeline.ipynb
Compare assembled traces files.ipynb		Compare assembled traces files.ipynb
Compare two excel files for data consistency.ipynb		Compare two excel files for data consistency.ipynb
Convert assembled traces to matlab workspace.ipynb		Convert assembled traces to matlab workspace.ipynb
Create average FoV.ipynb		Create average FoV.ipynb
Create grid of videos running in parallel.ipynb		Create grid of videos running in parallel.ipynb
Create visual representation of onset times.ipynb		Create visual representation of onset times.ipynb
Data Documentation Consistency Check.ipynb		Data Documentation Consistency Check.ipynb
Data Documentation Updates.ipynb		Data Documentation Updates.ipynb
Data Documentation to duckdb.ipynb		Data Documentation to duckdb.ipynb
Demo match LFP and Nikon.ipynb		Demo match LFP and Nikon.ipynb
Desperate matching of Nikon and Labview for T537 baseline.ipynb		Desperate matching of Nikon and Labview for T537 baseline.ipynb
Developing TwoPhotonSession.ipynb		Developing TwoPhotonSession.ipynb
Estimate TMEV imaging time.ipynb		Estimate TMEV imaging time.ipynb
Extract 15 min stimulation recordings.ipynb		Extract 15 min stimulation recordings.ipynb
Extract all mean traces.ipynb		Extract all mean traces.ipynb
Extract events from events_list.xlsx.ipynb		Extract events from events_list.xlsx.ipynb
Fig 1 Seizure and weight plots.ipynb		Fig 1 Seizure and weight plots.ipynb
Get calibrations for Nikon recordings.ipynb		Get calibrations for Nikon recordings.ipynb
Get seizure start time for recording.ipynb		Get seizure start time for recording.ipynb
Grid SD Analysis.ipynb		Grid SD Analysis.ipynb
High frequency voltage imaging extract trace.ipynb		High frequency voltage imaging extract trace.ipynb
Investigating the distance unit problem.ipynb		Investigating the distance unit problem.ipynb
Load CNMF.ipynb		Load CNMF.ipynb
Loco during seizure vs during SD TMEV.ipynb		Loco during seizure vs during SD TMEV.ipynb
Locomotion ChR2 waterfall.ipynb		Locomotion ChR2 waterfall.ipynb
Locomotion analysis 1.0.ipynb		Locomotion analysis 1.0.ipynb
Locomotion analysis 2.0.ipynb		Locomotion analysis 2.0.ipynb
Locomotion analysis 3.0.ipynb		Locomotion analysis 3.0.ipynb
Locomotion analysis development.ipynb		Locomotion analysis development.ipynb
Manual LabView-Nikon matching.ipynb		Manual LabView-Nikon matching.ipynb
Match spatial components test.ipynb		Match spatial components test.ipynb
Match v-EEG with video.ipynb		Match v-EEG with video.ipynb
Matlabize TwoPhotonSession.ipynb		Matlabize TwoPhotonSession.ipynb
Michael_dff.m		Michael_dff.m
Open results.ipynb		Open results.ipynb
Opening hdf5 results.ipynb		Opening hdf5 results.ipynb
Play nd2 along LFP, movement.ipynb		Play nd2 along LFP, movement.ipynb
Pre-post cell count.ipynb		Pre-post cell count.ipynb
README.md		README.md
Recovery analysis.ipynb		Recovery analysis.ipynb
RippleNoiseRemoval prototype.ipynb		RippleNoiseRemoval prototype.ipynb
RippleNoiseRemoval.py		RippleNoiseRemoval.py
SHA256.ipynb		SHA256.ipynb
Simultaneous SD and spiking activity.ipynb		Simultaneous SD and spiking activity.ipynb
Sliding bar time series with 2p recording.ipynb		Sliding bar time series with 2p recording.ipynb
Spectrogram of mean fluo.ipynb		Spectrogram of mean fluo.ipynb
Test Matlab Integration.ipynb		Test Matlab Integration.ipynb
Test average frame.ipynb		Test average frame.ipynb
Test hdf5 splitting.ipynb		Test hdf5 splitting.ipynb
Visualize color coding.ipynb		Visualize color coding.ipynb
Waterfall plot all seizures.ipynb		Waterfall plot all seizures.ipynb
Waterfall plotting stimulation experiments.ipynb		Waterfall plotting stimulation experiments.ipynb
Working with 2p session class.ipynb		Working with 2p session class.ipynb
Working with EDF files.ipynb		Working with EDF files.ipynb
checksum.py		checksum.py
cnmf_results.py		cnmf_results.py
convert_nikmeta.py		convert_nikmeta.py
datadoc_util.py		datadoc_util.py
demo_motion_correction.ipynb		demo_motion_correction.ipynb
demo_pipeline.ipynb		demo_pipeline.ipynb
demo_pipeline.py		demo_pipeline.py
h5_assembled_traces_to_workspace.m		h5_assembled_traces_to_workspace.m
io_2p.py		io_2p.py
loco_functions.py		loco_functions.py
match_recordings.py		match_recordings.py
motion_correction_split.py		motion_correction_split.py
movie_splitting.py		movie_splitting.py
mtime, ctime back up.ipynb		mtime, ctime back up.ipynb
multisession_registration.ipynb		multisession_registration.ipynb
nd2 to caiman.ipynb		nd2 to caiman.ipynb
nd2 to multipage tiff test.ipynb		nd2 to multipage tiff test.ipynb
nd2_to_caiman.py		nd2_to_caiman.py
place_coding.py		place_coding.py

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