This repository contains tools for analyzing synaptic connectivity data.
If you just want to be able to use the package and don't care about making any package modifications, you can install the package from git:
pip install git+https://github.com/alitwinkumar/connectome_tools.gitThis can be useful if you intend on editing or contributing to this package.
# clone the repo
git clone [email protected]:alitwinkumar/connectome_tools.git
cd connectome_tools
# Don't forget to activate your environment
[activate your environment]
# Install connectome_tools package as editable
pip install -e .The -e flag will make the package editable, so any changes made to the package will be reflected in python.
connectome_loaders.py contains functions that return synaptic connectivity for the Janelia hemibrain (Scheffer et al. 2020), larval connectome (Winding et al. 2023), and FlyWire (Dorkenwald et al. 2022) datasets. Function docstrings contain instructions for how to download the data.
shuffle.py contains code for degree-matched shuffling of connectivity matrices and analysis of singular value spectra as compared to shuffles.
filter_connectivity.py contains code for (efficiently in the case of sparse matrices) subselecting the connectivity matrix from filtered sets of pre and post synaptic neurons.
influence_metrics contains code for ranking neurons in a connectome graph based on influence in behaviorally-relevant pathways.