🟤OMERO Resources
OMERO Resources
OMERO Support for Bioimaging Data Management at reNEW
OMERO is a specialized, open-source bioimaging data management platform developed by the Open Microscopy Environment (OME). It is designed to support the storage, annotation, visualization, sharing, and analysis of complex, high-resolution microscopy data. At reNEW, OMERO will be deployed in Winter 2025 as a dedicated solution for managing the full lifecycle of imaging data generated by the center’s stem cell and biomedical research activities.
Why OMERO Matters for reNEW
As a research center focused on regenerative medicine and stem cell biology, reNEW generates vast amounts of high-content imaging data—from live-cell time-lapse microscopy to 3D confocal stacks and spatial transcriptomics. These datasets are large, heterogeneous, and often produced across different platforms, formats, and research groups. OMERO provides a centralized, FAIR-aligned system that addresses these challenges by:
Ingesting and standardizing raw image files in vendor-neutral formats
Storing associated experimental metadata, annotations, and region-of-interest (ROI) definitions
Enabling access-controlled sharing among collaborators within and across labs
Supporting structured archival for long-term preservation and data reuse
Integrating with analysis pipelines, visualization tools, and image-based AI workflows
Use Cases at reNEW
OMERO at reNEW will serve two primary functions:
Offboarding of Departing Researchers OMERO ensures that valuable microscopy datasets generated by researchers who leave the center remain well-organized, searchable, and reusable. This supports institutional knowledge continuity, prevents data loss, and ensures alignment with reNEW’s long-term data stewardship goals.
Integration into Active Research Workflows Beyond offboarding, OMERO is designed to support ongoing imaging-intensive projects. Researchers can ingest, manage, annotate, and share microscopy data in daily research activities. Benefits include:
Improved reproducibility through structured metadata capture
Enhanced data integrity via centralized, secure storage
Streamlined collaboration through controlled data access
Greater compliance with funder and publisher requirements for data transparency
Strategic Role within reNEW’s RDM Infrastructure
The deployment of OMERO complements and extends reNEW’s broader Research Data Management (RDM) ecosystem, which includes tools like REDCap, LabGuru, and structured N-drive storage. OMERO fills a crucial gap by bringing imaging data into compliance with FAIR principles and aligning with the data lifecycle expectations of funders such as Horizon Europe, the ERC, and the Novo Nordisk Foundation.
The OMERO system will be integrated with:
Local NAS at reNEW for short-term image staging
High-throughput imaging workstations for direct transfer and analysis
KU IT infrastructure (DanHPC, KU Datasets, Database Store) for long-term storage, backup, and access security
This infrastructure supports seamless progression from microscope to metadata-enriched archival and enables researchers to scale imaging projects while maintaining robust, compliant data management practices.
Support and Onboarding
If you are interested in using OMERO for your project, offboarding legacy imaging data, or integrating your workflows into the OMERO platform, please reach out for support or guidance.
Contact: Richard Dennis Data Steward, reNEW 📧 [email protected] 🕒 Available Wednesdays 14:00–15:00 or by appointment
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