Getting Started

First Steps with NL-BIOMERO

Access the Platform

After deployment, open OMERO.web at the address provided by your system administrator (sometimes on port 4080).

Note

Default credentials are set during deployment. Contact your system administrator for login details. Administrators must change default passwords immediately after first login β€” see Metabase Administration for the security setup.

Warning

Do not log out of OMERO while a job is running.

Logging out, or closing the browser without the session being kept alive, will terminate your active OMERO session. Any running import or analysis jobs that were started under that session may fail or become orphaned.

  • After closing the browser, a session remains active for the configured session timeout period (default: 7 days). Jobs submitted before closing will continue to run.

  • Logging out immediately ends the session, regardless of running jobs. If you need to step away, simply close the browser tab instead of logging out.

Administrators can adjust the session timeout via CONFIG_omero_sessions_timeout in the deployment .env file.

OMERO.biomero Interface

OMERO.biomero is a plugin inside OMERO.web that provides a unified interface for importing and analyzing imaging data. After logging in to OMERO.web, open the BIOMERO panel from the top navigation bar.

The interface has the following main areas:

Import

The Import section has subtabs:

Import Images

Browse your current group’s remote shared storage and start an in-place import to bring your data into OMERO without duplicating files on disk.

Monitor

Track the progress of your import orders. An embedded Metabase dashboard shows all active and completed imports for your group. Each import order is identified by a UUID shown in the table β€” use this UUID to find your imported data back in OMERO.web.

Analyze

The Analyze section has subtabs:

Run

Submit analysis jobs to the HPC cluster. The Run subtab itself has two sub-sections:

  • Image Workflows (default) β€” choose a workflow, select datasets or individual images from OMERO as input, configure workflow parameters, and submit.

  • Plate Workflows (BIOMERO β‰₯ 2.4.0) β€” plate-aware analysis that sends the entire plate as a single Zarr, preserving well and acquisition structure. Only plates can be selected as input. Only workflows configured as Zarr Plate Workflows by your administrator appear here.

Status

Track your submitted jobs and see their current state (queued, running, finished, failed). Each job is identified by a Workflow ID (UUID) shown in the dashboard. Once a job finishes, search for that UUID in OMERO.web to find your result images, which are imported automatically with full provenance metadata.

Next Steps

  1. Import Data β€” Use the Import β†’ Import Images tab to bring your microscopy data into OMERO

  2. Run Analysis β€” Open Analyze β†’ Run β†’ Image Workflows (or Plate Workflows for plates), choose a workflow, and submit

  3. Track Progress β€” Check Analyze β†’ Status to monitor running jobs; note the Workflow UUID for later

  4. View Results β€” Search for the Workflow UUID in OMERO.web to find your imported result images

  5. Analytics β€” Use Import β†’ Monitor or Metabase to explore import and workflow statistics

Platform Overview from the README

To get started with data:

  1. Web Import: Use the Importer tab in OMERO.biomero at http://localhost:4080/omero_biomero/biomero/

  2. OMERO.insight: Download the desktop client

    • Connect to localhost:4063

    • Login as root / omero

BIOMERO BIOMERO - BioImage Analysis

Checkout the BIOMERO documentation for detailed usage instructions.

Quick Workflow Example:

  1. Initialize Environment:

    • Run script: biomero > admin > SLURM Init environment...

    • β˜• Grab coffee (10+ min download time for a few workflow containers)

  2. Run Analysis:

    • Select your image/dataset

    • Run script: biomero > __workflows >SLURM Run Workflow...

    • Configure import: Change Import into NEW Dataset β†’ hello_world

    • Select workflow: e.g., cellpose

    • Set parameters: nucleus channel, GPU settings, etc.

OR

  1. OMERO.biomero Analyzer UI:

    • Use the Analyzer tab at http://localhost:4080/omero_biomero/biomero/?tab=biomero

    • Select your workflow: e.g., Cellpose

    • Add Dataset, select the image(s) you want to segment

    • Fill in the workflow parameters in tab 2, e.g. nuclei channel 3

    • Select desired output target, e.g. Select Dataset hello_world again (don’t forget to press ENTER if you’re typing it); and Run!

    • Track your workflow status at the Status tab

  2. View Results:

    • Refresh OMERO Explore tab (in the Data tab; http://localhost:4080/webclient/)

    • Find your hello_world dataset with generated masks