To use generalized transfer entropy, follow the setup instructions in GTE_Setup.md. You may also need the newest version of Matplotlib. Other dependencies include pandas, seaborn, scikit-image, scikit-learn, networkx, python-louvain, markov-clustering
pipeline.py: Wraps the TIFF data (specifically, coming as BIGTIFF data), uses Caiman to extract ROIs and their activity, and stores the data in HDF5 files.plot_CaBMI: Scripts to plot ROI activityanalysis_CaBMI.py: Analysis and plotting functions to run on HDF5 files created by the pipeline.utils_cabmi.py: Utility functions for the analysis scripts.utils_gte.py: Utility functions for running generalized transfer entropy.