Getting Started

First Steps with NL-BIOMERO

Access the Platform

After deployment, access these interfaces:

Default Login

Use the default credentials to get started:

  • Username: root

  • Password: omero

Warning

Change the default password immediately after first login for security.

Next Steps

  1. Import Data - See data-import for uploading images

  2. Run Analysis - See biomero-workflows for bioimage analysis

  3. View Results - Use the web interface to explore results

  4. Analytics - Use Metabase for advanced visualization

Platform Overview

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 - BioImage Analysis

Checkout the BIOMERO documentation for detailed usage instructions.

Quick Workflow Example:

  1. Initialize Environment:

    • Run script: slurm/init/SLURM Init environment...

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

  2. Run Analysis:

    • Select your image/dataset

    • Run script: slurm/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; 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