OMERO.biomero Plugin Administration

The OMERO.biomero plugin provides two administrative interfaces for managing the Importer (ADI) and Analyzer components. These admin screens are accessible from the OMERO.web interface and provide essential configuration options for system administrators.

Note

For technical details about the Metabase integration and container configuration, see Metabase Container.

Accessing Admin Interfaces

The admin interfaces are available through the OMERO.web plugin after logging in as an administrator:

  1. Navigate to the OMERO.biomero plugin in OMERO.web

  2. Select the “Admin” tab for Import or Analyze

Importer Admin Configuration

The Importer Admin tab manages settings for the Automated Data Importer (ADI).

Group Folder Mappings

Purpose: Restrict which OMERO groups have access to specific folders that the importer can import from.

Configuration: - Currently supports 1:1 mapping only - Each OMERO group can be mapped to one subfolder instead of the full mounted disk folder

Setup Process:

  1. Select the target OMERO group

  2. Choose the folder from the available options

  3. Save the mapping

Warning

Folder Selection Limitation: The folder selector only shows currently loaded subfolders (1st level).

Workaround: To select deeper subfolders:

  1. Go to the “Import Images” tab

  2. Navigate and expand the desired subfolder

  3. This loads sub-subfolders into ReactJS memory

  4. Return to Admin tab where they will now be selectable

Warning

Changes Not Visible Immediately: Don’t refresh (F5) to see changes. Instead:

  1. Log out and log in again

  2. Change “Select group” to a different group

  3. The mapping should take effect showing only the mapped subfolder as import options

Configuration File Management

Storage: Changes are written via Django API to a configuration file.

Environment Variable: OMERO_BIOMERO_CONFIG_FILE

  • Example: /opt/omero/web/OMERO.web/var/biomero-config.json

Docker Mount Example:

volumes:
  - "./web/biomero-config.json:/opt/omero/web/OMERO.web/var/biomero-config.json:rw"

Important: Ensure the container user has write access to this file.

Additional Settings: The configuration file contains more UI variables than what the Admin tab can modify directly.

Analyzer Admin Configuration

The Analyzer Admin screen is split into two sections: BIOMERO settings (left) and OMERO scripts (right).

Overview

Left Side: All BIOMERO settings in UI form Right Side: OMERO scripts, organized with admin scripts “Slurm Init” and “Slurm Check Setup” shown by default

Important Workflow: Major changes (like adding new workflows) require:

  1. Save settings in the left panel

  2. Run the “Slurm Init” script from the right panel

Configuration File Sharing

File: slurm-config.ini - shared between OMERO.web and BIOMERO worker

Recommended Setup:

# OMERO.web service
volumes:
  - "./web/slurm-config.ini:/opt/omero/web/OMERO.web/var/slurm-config.ini:rw"

# BIOMERO worker service
volumes:
  - "./web/slurm-config.ini:/opt/omero/server/slurm-config.ini:rw"

This allows OMERO.web to write changes while BIOMERO worker reads the current configuration.

Settings Interface Usage

Edit Mode: Click the pencil icon to make fields editable Saving: Click “Save Settings” to write changes to disk via Django API Undo: Use “Undo All Changes” to reset current modifications

Settings Categories

1. SSH Settings

SSH Alias: Configure the alias used by BIOMERO to connect to the Slurm cluster

  • Must reflect an existing SSH alias configured in the BIOMERO container

  • Used for headless connection to Slurm

2. Slurm Settings

Slurm Data Path: Storage location for OMERO I/O data on Slurm cluster Slurm Images Path: Storage location for container images Slurm Script Path: Storage location for Slurm job scripts Slurm Script Repository: (Optional) GitHub repository URL for custom Slurm scripts

Warning

Script Repository: Either use a repository with scripts for ALL workflows, or let BIOMERO generate scripts automatically (recommended). Only use custom repositories for advanced cases.

3. Analytics Settings

Danger

NOT RECOMMENDED FOR MODIFICATION

FOR ADVANCED USERS ONLY

Tracking: Controls BIOMERO 2.0 eventsourcing system

  • Warning: Disabling tracking breaks views/listeners and progress monitoring

  • Dependencies: Views/listeners create database tables from tracking records

  • Impact: Progress tables in OMERO.biomero web plugin depend on this system

4. Converters Settings

FOR ADVANCED USERS ONLY

Add Custom Converters:

  • Naming Convention: X_to_Y format (e.g., zarr_to_tiff)

  • Docker Image: Specify container image (e.g., cellularimagingcf/convert_zarr_to_tiff:1.14.0)

  • Default Behavior: BIOMERO generates zarr_to_tiff converter automatically

Warning

Manual Integration Required: Custom converters require additional script modifications:

  1. Modify Slurm Workflow script to use custom conversion

  2. Update Run Workflow script for user selection

  3. Ensure Slurm Remote Conversion script handles custom converter

5. Models Settings (Workflows)

Primary Function: Manage available workflows in BIOMERO

Adding New Workflows

Click “Add Model” and configure:

Name: No spaces (becomes folder name on Slurm) GitHub Repository: Versioned URL (e.g., https://github.com/user/repo/tree/v1.0.0) Slurm Job Script: Usually jobs/<name>.sh (auto-generated default) Additional Slurm Parameters: SBATCH options specific to this workflow

Common SBATCH Parameters

Add as <key>=<value> format (without -- prefix):

# GPU allocation
gres=gpu:1g.10gb:1

# Partition selection
partition=luna-gpu-short

# Memory allocation
mem=15GB

# Time limits (d-hh:mm:ss)
time=08:00:00

Editing Existing Workflows

Edit Model: Click pencil icon to modify settings Version Updates: Change GitHub Repository URL version Parameter Management: Add/edit/delete Additional Slurm Parameters Reset: “Reset values” button undos changes to specific model Remove: “Delete model” button removes workflow entirely

Save Requirement: Click “Save Settings” after modifications

Required Follow-up Actions

After model changes (except Additional Slurm Parameters):

  1. Save Settings first

  2. Run “Slurm Init” script - installs changes on Slurm cluster

  3. Verify with “Slurm Check Setup” - shows available/pending models

Slurm Check Setup Output

The “Slurm Check Setup” script provides:

  • Available Models (with versions)

  • Pending Models

  • Available Converters

  • Available Data

  • Singularity Log for download progress monitoring

Example Output:

starting cellpose v1.3.1
starting stardist v1.3.2
FATAL: Image file already exists: "cellpose/w_nucleisegmentation-cellpose_v1.3.1.sif" - will not overwrite
finished cellpose v1.3.1

Status Indicators: - FATAL: Image file already exists - Good (no redownload needed) - ERROR - Problem occurred - starting/finished - Normal download process

Security Considerations

Configuration Files: Ensure proper file permissions for mounted configuration files SSH Access: Verify SSH aliases and key access for Slurm connectivity Database Access: Confirm BIOMERO worker can access shared configuration files

For initial security setup including Metabase integration, see Metabase Container.

Troubleshooting

Changes Not Visible: Log out and back in instead of refreshing Slurm Connection Issues: Verify SSH alias configuration and key access Model Not Available: Run “Slurm Init” after adding/modifying workflows Permission Errors: Check file permissions on mounted configuration files

For Metabase-specific troubleshooting (e.g., “Message seems corrupt” errors), see Metabase Container.