JF Lab Pipeline for CHEndoscope Analysis

The JF-Lab pipeline for preprocessing and analysis of CHEndoscope calcium imaging data.

1. Get your .mkv files to be merged, downsampled and/or motion corrected.
2. Run the following on the .mkv files:
   python minipipe.py file1.mkv file2.mkv -c 2000 --motion_corr --cores 8
   Flags:
   -d/--downsample: temporal downsample factor, defaut=4
   -c/--chunk_size: chunk_size, default=2000
   --motion_corr: if you want to correct motion, default=False
   -t/--threshold: if you want to indicate threshold for motion correction, default=1.0
   -target_frame: if you want to indicate frame of reference for motion correction, default=0
   --cores: number of threads to run in parallel, default=4
   --bigtiff: If .mkv(s) amount to > 12Gb, must use this mode or memory error will occur
   --merge: merge all the files instead of individually processing them
   -o/--output: If --merge, then the name for the merged .tiff file
   -f/--format: output format as tiff or avi, default is tiffs
3. Run CNMF-E on the .tiff files, output is a .mat file.
4. Use review_traces.py to manually inspect the neurons to keep or exclude from analysis:
   python review_traces.py traces.mat

• Press 'k' to keep, 'j' to exclude, or the 'keep'/'exclude' buttons.