calcium_imaging

Tools to process calcium imaging data, including exporting images to videos, and analyzing videos via Suite2P

The pipeline runs in the following order:

1. create_bigtifs_multiple_folders.py takes a filepath as input and calls tif_to_video.py, which takes .TIF images as input and exports TIF stacks in bigTIFF format
2. suite2p_script.py runs Suite2P on these bigTIFF stacks, and the outputs of Suite2p are all numpy arrays described (here)[https://suite2p.readthedocs.io/en/latest/outputs.html]. The most important of these outputs is spks.npy, which contains the final deconvolved time series of all regions of interest (ROIs; i.e., cells and non-cells).
3. subset_spks_cellROIs.py searches for all spks.npy files and subsets the cell ROIs to produce cell_spks.npy.