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OMERO–HPC Integration Scripts

This repository contains the set of Python scripts that must be deployed on the OMERO server in order to interact with the HPC environment for Biom3d used for bio-imaging workflows.
They handle tasks such as:

  • Submitting preprocessing and training jobs to the HPC scheduler (Slurm).
  • Managing dataset and project metadata inside OMERO.
  • Ensuring results produced on the HPC are stored back into OMERO in a reproducible way.

Dev

  • Sami Safarbati – Institut de Génétique, Reproduction et Développement (iGReD), UCA, CNRS, Clermont-Ferrand, France; Institut Pascal, UCA, CNRS, Aubière, France.

  • Pierre Pouchin – Institut de Génétique, Reproduction et Développement (iGReD), UCA, CNRS, Clermont-Ferrand, France.

Usage

  1. Place the scripts in the appropriate OMERO server directory (typically alongside user scripts in lib/scripts or the configured scripts path).
  2. Ensure the OMERO server has permission to submit jobs to the HPC (via the dedicated omero system user).
  3. Configure the HPC job submission settings (slurm accounts, GPU access, temporary scratch paths, etc.) according to your environment.
  4. From OMERO.web, users can trigger the scripts, which will handle the HPC job lifecycle transparently.

Notes

  • All jobs are submitted under the omero system user on the HPC(for our use case). This ensures consistency regardless of which OMERO user triggers the job.
  • The omero account must have access to GPU nodes and the correct Slurm accounts configured.
  • The code is designed for reproducibility and transparency: all datasets and results are traceable in OMERO.