The script exceptions.py was added to better handle and manage exceptions in the data set, such as: 1) missing tiles for a given channels and 2) missing reference marker for a whole acquisition, e.g. DAPI.
1.1.0
1) Installation of basicpy via RUN pip install in the Dockerfile 2) Added the -ic flag in the CLI to call the illumination correction on the tiles 3) If the -ic flag is used, the output images will have the prefix "corr" in the name. 4) Added the -od argument to specify the name of the deepest output directory. Default value is "raw" to make it compatible with MCMICRO.
1.0.0
Python scripts to stage MACSima data for ASHLAR/MCMICRO