labsyspharm/basic-illumination repository overview

⁠basic-illumination

ImageJ BaSiC shading correction for use with Ashlar

⁠Running as a Docker container

Create a container:

docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash

where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container.

Once inside the container, do ls /data to ensure your data is there, followed by

ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
  "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"

for each input.ome.tiff in your data directory.

(Note that the trailing \ on the first line is necessary to break the command up across multiple lines. When writing the command on a single line, the \ should be removed to avoid parse errors.)