Written by David James Estrin. If using this code, please kindly cite (Estrin et al., 2024 unpublished). This repository was written to analyze light sheet data on a SLURM based high performance cluster. Pieces of this pipeline originate from other code repositories which have been cited accordingly below.

The pipeline consists of the following steps: (1) Moving the data to a scratch drive (2) Denoising/destriping the data via Pystripe (https://github.com/chunglabmit/pystripe) (3) Stitching the data via terastitcher (https://github.com/abria/TeraStitcher) (4) Registering images to allen brain atlas (https://github.com/neurodata/CloudReg) (5) Segmenting pixels and counting cells (cells, axons, etc) (loosely based on brainlit: https://github.com/neurodata/brainlit using ilastik: https://github.com/ilastik/ilastik). (6) calculating the number of counts per region, generating statistics and relevant pictures.