labsyspharm/basic-illumination
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ImageJ BaSiC shading correction for use with Ashlar
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.)
docker pull labsyspharm/basic-illumination