Whole Brain Freely Moving Tracking and Trace extraction

Contains code for the pipeline, GUI, and analysis code for the paper: An intrinsic neuronal manifold underlies brain-wide hierarchical organization of behavior in C. elegans

This repository contains python code for analyzing raw volumetric images in two channels: red (tracking) and green (activity). Behavior analysis is also included as optional analysis, and is in a separate repository

In order to reproduce the paper figures, please see the exported jupyter notebooks here. Note that the raw data is needed, and thus any code related to loading the data would need to be updated to properly run these scripts.

Installation

This project is designed to be installed with Anaconda, but we suggest using mamba. There are different use cases, some of which have easier installation steps. Please check all sections below to determine which is best for you.

Just running the GUI

See GUI README

Running the full pipeline (non-Zimmer)

See: Running the pipeline

Dev installation (local, for editing)

This is for developers, or if you want to run the full pipeline on your local machine. See: detailed installation instructions

Running the full pipeline (Zimmer lab)

If you just want to run the pipeline (most people), then you can use the pre-installed environments installed on the cluster, which can be activated using:

conda activate /lisc/data/scratch/neurobiology/zimmer/.conda/envs/wbfm/

Running the pipeline

See: Running the pipeline

Summary of GUIs

All guis are in the folder: /folder_of_this_README/wbfm/gui/example.py

1. Initial creation of project.

python wbfm/gui/create_project_gui.py

See: Running the pipeline for fields to check after creating a new project

2. Visualization of most intermediate steps in the analysis is also possible, and they can be accessed via the progress gui. This also tells you which steps are completed. Note that the progress checking doesn't work with nwb files, but the gui does:

python wbfm/gui/progress_gui.py

Or, if you know the project already:

python wbfm/gui/progress_gui.py --project_path PATH-TO-YOUR-PROJECT

3. Manual annotation and more detailed visualization. Note, this can take minutes to load:

python wbfm/gui/trace_explorer.py --project_path PATH-TO-YOUR-PROJECT

FAQ, including fixes for common problems

FAQ

Please also check (via search) the open and closed issues on github.

More details

Detailed pipeline steps

Detailed installation instructions

Known issues

Folder organization

If you would like to contribute, see how to contribute