Imaging softwares

Feel free to propose new services using pull requests, or to request them by creating new issues.

CellProfiler

Cell image analysis software. See their website.

You can start a container using the CellProfiler template in the Catalog web UI (make sure the Templates checkbox is checked)

This template uses the official CellProfiler image hosted on DockerHub

Persistent data folder

📂 Use the /usr/local/src/work folder (home of the root user) to store your data in the existing persistent storage. You can find the persistent volumes in the DSRI web UI, go to the Administrator view > Storage > Persistent Volume Claims.

Once the CellProfiler has been started you can access it through the pod terminal (in the DSRI web UI, or using oc rsh POD_ID)

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