Bioimaging data management: Platform deployment support through central infrastructure projects

The volume and complexity of data generated with modern bioimaging technologies pose significant challenges to sustainable data management and reuse. While the FAIR principles (Findable, Accessible, Interoperable, Reusable) are recognized as essential to ensuring the long-term value of such data, practical implementation remains challenging for individual universities or research institutions. One key barrier is the lack of local expertise and dedicated staff to design and operate research data infrastructure tailored to the specific needs of bioimaging data. The Information Infrastructure for BioImage Data (I3D:bio) project addresses this critical gap in the German research landscape by offering hands-on, tailored support for the deployment of local data management infrastructure for microscopy data focusing on OMERO, a widely used open-source image data management platform. OMERO is an open-source software that is well-established in the bioimaging community. It offers user-friendly, web-based data exploration and annotation as well as figure-creation and data sharing. OMERO has been used in public repositories for bioimaging data and can be configured to expose public data from individual institutions' instances for sharing and reuse. Through a guided approach, the I3D:bio team assists institutions with the installation, configuration, and initial population of their OMERO servers. This includes advice on the stakeholder process, infrastructure requirements, user access strategies, metadata annotation (e.g., with REMBI-compliant key-value pairs), and long-term sustainability. By lowering the barrier to entry, this model has led to successful OMERO deployments at various institutions during the project's first funding phase, of which we exemplify a key use case from the Technical University of Dresden. Here, we present lessons learned from these deployments. We will share insights into pitfalls encountered by the involved stakeholders and new OMERO users, including challenges in metadata harmonization, and training, as well as the solutions developed in response by the I3D:bio team. The effectiveness of a structured, collaborative deployment pathway has made I3D:bio a valuable catalyst for building capacity and enabling scalable imaging data infrastructures at the institutional level.