Supplementary data for minian paper

This repository contains the data and code used to generate Figure 1-15 and Figure 20 of the manuscript "Minian an Open-source Miniscope Analysis Pipeline"

repo content

• data/ contains raw and intermediate data.
• minian_snapshot/ contains a copy of minian that's used for analysis.
• ezTrack_snapshot/ contains a copy of ezTrack that's used for analysis.
• figs/ contains all the generated figures.
• misc/ contains some simple script to generate the dependency table used in the paper.
• concat_video.ipynb concatenate behavior videos so they can be easily processed with ezTrack.
• cross-registration.ipynb is a modified version of minian notebook that register cells across sessions.
• cross-registration_shuffle.ipynb is a modified version of minian notebook that shuffle the location of cells (spatial footprints) and generated cell mappings across sessions.
• pipeline_paper.ipynb is a modified version of minian pipeline to facilitate taking snapshot of visualizations.
• place_cell.ipynb / place_cell.py extracts place cells from neural activities based on critirias.
• validate.py generate a validation plot that is now obsolete.
• validate_plc.py validate spatial firing pattern of place cells across original and shuffled cell mappings and generate fig 20.
• flow_chart.py generate the flow chart of the pipeline (fig 1).

steps to reproduce

create environments

1. conda env create -n minian_paper_data -f misc/encironment.yml

get data

The source data are hosted on figshare. We have a convenient script to retrieve all the necessary data.

1. python get_data.py

reproduce figure 1

1. python flow_chart.py

reproduce figure 2-15

Run through pipeline_paper.ipynb and use the developer tool in the browser (preferrable google chrome) to take snapshot with a specific size.

reproduce figure 20

rerun minian and ezTrack processing (Optional)

Since all the intermediate data are retrieved with get_data.py under ./data/inter, this section can be skipped if you just want to reproduce plotting of Figure 20.

1. run through ./concat_video.ipynb and then ./ezTrack_snapshot/LocationTracking_BatchProcess.ipynb to produce location tracking results.
2. for each pipeline.ipynb under ./data/pfd2, change minian_path to "../../../minian_snapshot" and run through the notebook to reproduce minian results.
3. run through ./cross-registration.ipynb and ./cross-registration_shuffle.ipynb to reproduce cross registrationi results.
4. run through ./place_cell.ipynb to classify place cells.

reproduce figure 20

1. python validate_plc.py