Getting Started

First Steps with NL-BIOMERO

Access the Platform

After deployment, access these interfaces:

• OMERO.web: http://localhost:4080 - Login: root / omero (change default password)

• Metabase: http://localhost:3000 - Login: admin@biomero.com / b1omero (change default password)

Default Login

Use the default credentials to get started:

• Username: root

• Password: omero

Warning

Security Setup Required: Change default passwords and configure security settings immediately after first deployment.

For OMERO: Change the default password after first login.

For Metabase: Follow the complete security setup procedure in Metabase Container which includes changing passwords, updating database connections, and regenerating security keys.

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

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🧬 BIOMERO - BioImage Analysis

Checkout the BIOMERO documentation for detailed usage instructions.

Quick Workflow Example:

1. Initialize Environment:

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

   • ☕ 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 → hello_world

   • Select workflow: e.g., cellpose

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

OR

2. 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

3. View Results:

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

   • Find your hello_world dataset with generated masks

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