I3D:bio - Information Infrastructure for BioImage Data

• Applicants: Dr. Karen Bernhardt; Professorin Dr. Elisa May; Dr. Roland Nitschke; Professorin Dr. Stefanie Weidtkamp-Peters
• Term: since 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 462231789

Microscopy has been instrumental to many breakthrough discoveries in the life sciences for the last two centuries. But it's just recently that a wave of technological innovations has transformed microscopy from a low-throughput, qualitative technique for visualizing biological samples into a big-data, quantitative analytical tool delivering insights at the molecular level. This massive data will unfold its full potential only if it becomes available to the whole scientific community. By reproducing, comparing, and re-analyzing, researchers will generate new knowledge from existing bioimaging data. A prerequisite for the community-wide exchange of bioimaging data is the adoption of the FAIR principles of data management: data is stored in open formats, linked to experimental details via metadata that can be read and correctly interpreted, and all information is stored in open access public archives. We propose to create I3D:bio, an infrastructure that addresses these challenges and brings FAIR practices for bioimage data management at the hand of German researchers. Connecting these scientists to initiatives for a pan-European bioimage data infrastructure will also be a goal of I3D:bio, together with providing a framework for international collaborations on standards for bioimage data formats and public bioimage repositories. I3D:bio will begin as an infrastructure offering services based on OMERO, an open-source platform for visualizing, managing, and annotating scientific image data. Users of I3D:bio will be provided with target group-specific and user-oriented guidelines for installing OMERO as a central institutional resource, will receive tools for the convenient annotation of their bioimage data using controlled vocabularies, and the support to apply them effectively. I3D:bio will provide an OMERO database containing reference images and protocols for the quality assessment of microscope performance, and tools for integrating OMERO in electronic lab books. I3D:bio will become a platform for communication and training in bioimage data management. Its resources will be openly available to the whole scientific community. For building I3D:bio we will take advantage of the network of imaging facilities and research groups of German BioImaging- Gesellschaft für Mikroskopie und Bildanalyse. A significant number of collaborators belonging to different German research organisations, of which some have already established OMERO at their institutions, have declared their interest in contributing to this effort because they see the benefit of a coordinated approach to bioimage data management in Germany. Furthermore, we will closely follow the development of the National Infrastructure for Research Data, NFDI. Several consortia that will conduct bioimaging-based research projects have expressed their interest in the services of I3D:bio. We envisage that I3D:bio may become a reference entity for bioimage data management within the NFDI.

• DFG Programme: Research data and software (Scientific Library Services and Information Systems)
• Co-Investigator: Susanne Kunis