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BIOMERO Videos

This page is the canonical collection of NL-BIOMERO videos and their supporting text. Start with the conceptual introduction if BIOMERO, OMERO, or HPC is new to you. If you already know OMERO, the shorter architecture clips explain the technical boundaries and data flows.

Conceptual introduction

BIOMERO explained: a conceptual introduction

Purpose: A seven-minute introduction to the FAIR data challenge, OMERO data management, and the way BIOMERO connects image data to reproducible analysis.

Duration: approximately 7 minutes

For newcomers: No prior knowledge of OMERO or HPC is required.

Note

Production note: This conceptual overview was generated with Google NotebookLM using NL-BIOMERO’s GitHub repositories, documentation, and project publications available at the time of production. It was reviewed by the project team before publication. The video is intended as an accessible introduction; the current documentation remains authoritative for technical details and subsequent developments.

Summary

Bioimaging produces more data than manual approaches can reliably organize and reproduce. OMERO centralizes image data, metadata, and access, while BIOMERO 1.0 connects OMERO to containerized analysis on HPC. BIOMERO 2.0 extends that bridge with guided importing, a unified web interface, automated result return, and provenance captured throughout the workflow. Together these components make data and analyses easier to find, access, reproduce, and reuse.

Read the technical documentation: Architecture Overview

Technical architecture clips

These short clips focus on one architectural idea at a time. The system-boundary clip comes first because it provides the orientation needed for the other topics.

What NL-BIOMERO adds to OMERO

Purpose: See where OMERO ends and the importer, analyzer, web interface, and monitoring services supplied by NL-BIOMERO begin.

Duration: 1 minute 26 seconds

Summary

OMERO remains the central image-data, metadata, and access-control system. NL-BIOMERO surrounds it with OMERO.biomero for user-facing import and analysis, BIOMERO.importer for storage-aware ingestion, BIOMERO.analyzer for HPC execution, and Metabase for monitoring. BIOMERO.db records import and analysis events and provides the provenance and live status views used by those services. NL-BIOMERO connects this surrounding infrastructure rather than replacing OMERO.

Read the technical documentation: Architecture Overview

One format, flexible workflows

Purpose: Understand how a consistent OME-Zarr transfer path can still serve workflows that consume TIFF, Zarr, or plate-aware Zarr input.

Duration: 58 seconds

Summary

Regardless of whether OMERO data originated as CZI, LOF, TIFF, or another supported format, BIOMERO exports the selected pixels as OME-Zarr. Bilayers workflows can consume this directly. BIAFLOWS workflows that expect TIFF can first use an optional Zarr-to-TIFF conversion job on Slurm. Auxiliary attachments can accompany the image input, while images and file outputs return to OMERO.

Read the technical documentation: Analysis Pipeline and Zarr and Plate Workflow Types

In-place importing

Purpose: Learn how NL-BIOMERO registers data from shared storage in OMERO without making another copy of the original files.

Duration: 1 minute 24 seconds

Summary

The selected OMERO group determines which remote-storage folder a user can browse. A selected file or dataset becomes an asynchronous import order and can optionally pass through a versioned preprocessing container. OME-Zarr can be imported directly. The original data remains on shared storage, while the web uploader provides a side entrance for individual files before starting the same import route.

Read the technical documentation: In-Place Import Pipeline and Analyzer → Importer Integration

Provenance while the work happens

Purpose: See how BIOMERO captures progress and provenance during imports and analyses rather than trying to reconstruct the history afterward.

Duration: 1 minute 26 seconds

Summary

OMERO.forms preserves structured metadata and its form version. Import orders record their source, requester, and preprocessing details, while workflow runs record inputs, versions, parameters, Slurm identifiers, progress, status, and results. BIOMERO.db stores these changes as immutable events and derives query-friendly views for live import and workflow progress, result links, and later inspection.

Read the technical documentation: Monitoring and Analytics and Metabase Container

Adding an analysis workflow

Purpose: Follow the path from a versioned workflow container and descriptor to an analysis that users can run from OMERO.biomero.

Duration: 1 minute 26 seconds

Summary

A workflow combines a versioned headless container with an explicit interface: a BIAFLOWS descriptor.json or Bilayers config.yaml. BIOMERO uses this metadata to construct the parameter interface and normally generate the Slurm job. After an administrator registers and initializes the pinned workflow version, users can run it through OMERO.biomero.

Read the technical documentation: Adding Your Workflow to BIOMERO

Note

Production and media note: These technical clips were created with AI assistance using original NL-BIOMERO artwork and human-reviewed technical content. The animations were rendered programmatically, and the original soundtrack was synthesized without third-party audio samples.

Live demonstration

NL-BIOMERO in practice

Purpose: See how users select data, run an analysis workflow, and inspect results in a working NL-BIOMERO deployment.

Presenter: Torec Luik, NL-BioImaging / Amsterdam UMC

Duration: 5 minutes 39 seconds

Note

Recorded demonstration (April 2026). The current interface remains broadly similar, but now includes additional functionality such as the web uploader and Bilayers workflows. Some dialogs, including the analysis output dialog, have also been updated.

Watch the demonstration on YouTube.

The presentation was recorded for the Euro-BioImaging Image Data Community Days 2026 ToolsExchange session. It is an authentic demonstration of the platform, not a complete tour of every feature in the current interface.

Continue with the documentation: Getting Started