rtubelleza/cast

Connectome Analysis and Simulation Toolbox

Summary

This a set of Python packages (.py files) useful for the processing, analysis and simulation of datasets from the neuPrint ecosystem (https://neuprint.janelia.org/). This was mainly for a research project, where I explored using the connectome dataset for retrieving premotor and motor neuron clusters, as well as simulated the entire VNC (MANC) as a virtual nervous system, generating in-silico data. The script used for simulations under many parameters and settings are found in param_search.py.

Documentation for classes within the packages are a current work in progress.

Example usage for how to process the data using the ConnDF class witinh the data_analysis.py package are provided in cast_example.ipynb. More updates to this notebook will be added, such as how to use the analysis packages, run neuron clustering and run the interative UI within this class.

Dependencies

As these are mostly wrapper classes, they rely on various Python packages. It is therefore highly recommended to construct a conda environment dedicated for using CAST. An environment.yml file containing a sample environment with the necessary packages is provided.