BIOMERO 2.0: end-to-end FAIR infrastructure for bioimaging data import, analysis, and provenance

TL;DR

BIOMERO 2.0 enhances the OMERO platform to be FAIR-compliant by integrating data import, analysis, and provenance tracking, enabling traceable and reusable bioimaging workflows through containerized components and dashboards.

Contribution

It introduces a comprehensive, FAIR-compliant bioimaging platform with integrated provenance tracking, combining data import, preprocessing, analysis, and workflow monitoring within OMERO.

Findings

Supports real-time provenance recording and visualization

Facilitates in-place data import with metadata enrichment

Enables containerized analysis on HPC systems

Abstract

We present BIOMERO 2.0, a major evolution of the BIOMERO framework that transforms OMERO into a FAIR-compliant (findable, accessible, interoperable, and reusable), provenance-aware bioimaging platform. BIOMERO 2.0 integrates data import, preprocessing, analysis, and workflow monitoring through an OMERO.web plugin and containerized components. The importer subsystem facilitates in-place import using containerized preprocessing and metadata enrichment via forms, while the analyzer subsystem coordinates and tracks containerized analyses on high-performance computing systems via the BIOMERO Python library. All imports and analyses are recorded with parameters, versions, and results, ensuring real-time provenance accessible through integrated dashboards. This dual approach places OMERO at the heart of the bioimaging analysis process: the importer ensures provenance from image acquisition through preprocessing and import into OMERO, while the analyzer records it for downstream processing. These integrated layers enhance OMEROs FAIRification, supporting traceable, reusable workflows for image analysis that bridge the gap between data import, analysis, and sharing.