zhuanglab/scmos repository overview

This image will run sCMOS analysis. You use it like this (at least on linux):

cd /path/to/directory/with/STORM/data
docker run -u `id -u`:`id -g` -v $(pwd):/data -e SCMOS="--movie movie_name.tif --bin movie.hdf5 --xml settings.xml" zhuanglab/scmos

The -u flag sets user:group to the current user and group. If you don't use this all the results files will be root:root. The -v flag specifies the local volume to mount as the 'data' volume in the docker container. It needs to be an absolute path. The -e flag specifies the environment, the SCMOS environment variable contains the command line options that will be passed to storm_analysis/sCMOS/scmos_analysis.py