Analysis of calcium imaging data recorded in the fruit fly

How to use this repo

For more information on the structure of this repo, see this template repo.

Analysis pipelines

The script files scripts/*.py are workflows to analyse imaging data.

script file	use case
full_pipeline.py	start-to-finish analysis pipeline merging raw data, ImageJ ROIs, ball velocities, and behavior

old scripts

These old scripts need to become part of the new code structure.

• scripts/old_notebooks/ca_imaging_stim.ipynb
• scripts/old_notebooks/ca_imaging.ipynb
• scripts/old_notebooks/focused_heatmaps.ipynb
• scripts/old_notebooks/hacky_aligned_behavior.ipynb
• scripts/old_notebooks/pretty_plot.ipynb

Installation

# create conda environment with necessary dependencies
conda create -n imaging_analysis -f environment.yml

# get source code
git clone https://github.com/bidaye-lab/imaging_analysis

# install code as local local python module
cd imaging_analysis
pip install -e .

# create notebooks
python src/create_notebooks.py

Update

# pull from github
cd imaging_analysis
git pull origin main

# recreate notebooks
conda activate imaging_analysis
python src/create_notebooks.py