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Imaging Software

CellProfiler​

CellProfiler is a cell image analysis tool for measuring and analyzing cell morphology and phenotypes from microscopy images.

Deploy​

Find the CellProfiler template in the DSRI Catalog (make sure the Templates checkbox is checked) and instantiate it. The template uses the official CellProfiler image from DockerHub.

Persistent storage​

Use the /usr/local/src/work folder to store your data. You can find the persistent volumes in the DSRI web UI under Administrator view > Storage > Persistent Volume Claims.

Particularities​

CellProfiler runs in headless mode on the DSRI. Access it via the pod terminal in the DSRI web UI, or using:

oc rsh <pod-name>

Then run CellProfiler from the terminal:

cellprofiler --help
cellprofiler --run
cellprofiler --run-headless

For more information on using CellProfiler from the command line, see this guide.