Post-acquisition processing pipelines for light-sheet microscopy

This script is for performing routine post-acquisition processing of raw images obtained from light-sheet microscopes. The pipeline is built on Snakemake and each step relies on other scripts developed in Chung Lab.

conda create -n pacqproc --file environment.yaml

This command will create an isolated conda environment named pacqproc and install all the dependencies listed in environment.yaml.

Please edit config.yaml to configure the pipeline. You can specify which workflow to use, data path, channels, labels, and so forth.

snakemake -j

This will simply run all the necessary steps with all available cores. If you want to limit the number of cores, use -c [#cores] flag instead of -j.

Please refer to this for more complicated options.