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. For Metabase administrative setup and security configuration, see Metabase Administration.

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 BIOMERO.importer (formerly 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

Note

Zarr workflow support (see Zarr and Plate Workflow Types below) requires BIOMERO ≥ 2.4.0 and biomero.scripts ≥ 2.4.0, and depends on the BIOMERO.analyzer + BIOMERO.importer Integration integration being enabled first (IMPORTER_ENABLED=true).

The Analyzer Admin screen is split into two sections: BIOMERO.analyzer 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 Management

File Management: The Admin interface manages the slurm-config.ini file automatically.

For container mounting and file sharing setup, see BIOMERO.analyzer SLURM Integration for NL-BIOMERO.

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

SSH Settings

SSH Alias Field: Enter the SSH alias name for your SLURM cluster connection.

Note

The alias must match an entry in your SSH config. For SSH setup and configuration details, see BIOMERO.analyzer SLURM Integration for NL-BIOMERO.

SLURM Settings

Slurm Data Path: Path where OMERO data will be stored on the cluster

Slurm Images Path: Path where workflow container images are stored

Slurm Script Path: Path where job scripts are generated and stored

Slurm Script Repository: (Optional) Custom GitHub repository for job scripts

Warning

Script Repository: Leave empty to use auto-generated scripts (recommended). Only specify for advanced custom script repositories.

Analytics Settings

Danger

Advanced Users Only - Do Not Modify

Tracking Checkbox: Controls the BIOMERO eventsourcing system

Warning

Disabling tracking will break progress monitoring and result displays in the web interface.

Converters Settings

For Advanced Users Only

Add Converter Button: Click to add custom data converters

Name Field: Use X_to_Y format (e.g., zarr_to_tiff)

Docker Image Field: Specify the container image URL

Warning

Custom converters require additional integration work. Most users should rely on built-in converters.

Models Settings (Workflows)

Purpose: Add and manage analysis workflows available to users

Adding New Workflows

  1. Click “Add Model” to create a new workflow entry

  2. Configure Fields:

    • Name: Workflow identifier (no spaces)

    • GitHub Repository: Versioned URL to workflow code

    • Slurm Job Script: Job script path (usually auto-generated)

    • Additional Slurm Parameters: Custom SBATCH options for this workflow

    • Zarr Workflow (BIOMERO ≥ 2.4.0): Toggle on if the workflow expects a Zarr file as input. BIOMERO skips the usual TIFF conversion and passes the Zarr directly to the SLURM job. Requires the BIOMERO.analyzer + BIOMERO.importer Integration integration to be enabled.

    • Zarr Plate Workflow (BIOMERO ≥ 2.4.0): Toggle on if the workflow expects an entire plate as a single Zarr. Only plates can be submitted as input (no datasets). Enables the dedicated Plate Workflows tab in the analyzer UI. Requires the BIOMERO.analyzer + BIOMERO.importer Integration integration to be enabled.

  3. Save Settings to store the configuration

Common SBATCH Parameters

Format: Enter as key=value pairs (without -- prefix)

Examples:

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

  • Partition selection: partition=luna-gpu-short

  • Memory allocation: mem=15GB

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

Editing Existing Workflows

Edit Model: Click the pencil icon next to a workflow to modify its settings

Version Updates: Change the GitHub Repository URL to update workflow versions

Parameter Management: Add, edit, or delete Additional Slurm Parameters

Reset Changes: Use “Reset values” button to undo modifications to a specific workflow

Remove Workflow: Click “Delete model” to remove a workflow entirely

Important

Always click “Save Settings” after making any modifications.

Required Follow-up Actions

After model changes (except Additional Slurm Parameters and Zarr toggles):

  1. Save Settings first

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

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

Note

The Zarr Workflow and Zarr Plate Workflow toggles take effect immediately after saving — they control BIOMERO’s input preparation on the web side and do not require a Slurm Init run.

Zarr and Plate Workflow Types

From BIOMERO v2.4.0 onward (requires biomero.scripts ≥ 2.4.0 and the BIOMERO.analyzer + BIOMERO.importer Integration integration enabled), each workflow in the Admin can be toggled as a Zarr-based workflow. This changes how BIOMERO prepares input data and which UI options users see.

Important

Both Zarr options require the BIOMERO.analyzer + BIOMERO.importer Integration integration (IMPORTER_ENABLED=true). Without it, enabling these toggles has no effect.

Zarr Workflow

When Zarr Workflow is enabled for a model:

  • The user’s input images are exported from OMERO as a Zarr file.

  • BIOMERO skips the usual TIFF conversion step — no converter runs.

  • The Zarr is placed in the SLURM job’s input directory as-is.

Use this for workflows written to consume Zarr input directly rather than a flat folder of TIFF images. Standard BIAFLOWS workflows (which expect a folder of TIFFs) are not compatible with this option.

Zarr Plate Workflow

When Zarr Plate Workflow is enabled for a model:

  • The workflow can only be submitted with plates as input (no datasets).

  • The entire plate is packaged as a single Zarr that preserves the full plate structure: wells, fields inside the wells, and metadata.

  • No conversion is performed; the plate Zarr is passed directly to the SLURM job.

  • The (image) output is expected to be a Zarr plate as well, which BIOMERO will import back into OMERO while preserving plate structure - specifically the labels subdirectory ( https://ngff.openmicroscopy.org/0.5/#labels-md ) images will be in-place imported (if available)

Why this matters: Previously, submitting a plate for analysis caused BIOMERO to treat it as a dataset — a flat folder of individual images, losing all plate structure (wells, etc.). Zarr plate mode preserves the complete hierarchy, enabling workflows that need to reason about well positions or plate-level metadata.

Dedicated UI tab: Zarr plate workflows appear under a separate Plate Workflows tab in the analyzer interface, distinct from the standard dataset-based workflow tab. The submission dialog for plate workflows only allows selecting plates as input and output targets — datasets are not shown.

Warning

Zarr plate workflows are not compatible with standard BIAFLOWS workflows. Those workflows read a flat folder of TIFF images and have no awareness of the Zarr plate format. A workflow must be specifically written to read the Zarr plate structure (wells, acquisitions) in order to work with this option.

BIAFLOWS descriptors and Zarr auto-detection

BIAFLOWS workflows do not support Zarr natively. By design, a BIAFLOWS workflow consumes a flat folder of TIFF images as input. This is an implicit convention of the BIAFLOWS / cytomine-0.1 descriptor format — the descriptor specification does not carry any file-type constraint field.

This has two practical consequences:

  1. No auto-detection: BIOMERO cannot read a BIAFLOWS descriptor.json and automatically determine whether a workflow expects TIFF or Zarr input. The Zarr toggles in the Admin UI therefore exist as an explicit, manual configuration choice made by the administrator - not something inferred from the descriptor.

  2. Full descriptor compatibility: The cytomine-0.1 descriptor format is read and understood by BIOMERO for everything else (parameters, metadata, versioning). Marking a workflow as Zarr in the Admin UI simply overrides how BIOMERO stages input data before submitting the SLURM job; it does not require any changes to the descriptor itself.

Note

Future direction: BIOMERO is investigating support for a second descriptor schema - most likely a subset of CWL (Common Workflow Language) - that does explicitly declare accepted file types and formats. When this is available, BIOMERO will be able to auto-detect and validate Zarr compatibility from the descriptor, removing the need for the manual toggles. This is a work in progress (TBC).

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

Interface Troubleshooting

Changes Not Visible: Log out and log back in instead of using browser refresh

Folder Selection Issues: Navigate to Import Images tab first to load subfolders, then return to Admin tab

Model Not Available After Adding: Run the “Slurm Init” script after saving new workflow configurations

For SLURM connection, SSH, and deployment issues, see BIOMERO.analyzer SLURM Integration for NL-BIOMERO.

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