Use Case Report about Setting up an institutional OMERO system published
As the main use case of our partner project Information Infrastructure for BioImage Data (I3D:bio), the Core Facility Cellular Imaging at the TU Dresden Medical Faculty has implemented a new OMERO instance over the course of the past two years. The RSE team and the Data Stewardship team from NFDI4BIOIMAGE contributed to this use case through supporting the inegration of existing Fiji Macros, and helping with REMBI-compliant metadata annotation. Find the full use case report now published at the Journal of Microscopy.
Setting up an OMERO instance from scratch requires careful planning, and local cooperation across departments. The Core Facility Cellular Imaging (CFCI) at TU Dresden Medical Faculty has volunteered to act as the "naive site" for implementing a new OMERO instance with support from the I3D:bio project. During the pilot phase of the new OMERO instance, the CFCI has included several pilot projects using a variety of imaging modalities. While the I3D:bio project partners have supported the project from planning over installation, server maintenance, and training, members of NFDI4BIOIMAGE contributed with support on applying existing Fiji Macros to the new OMERO workflow as well as supporting REMBI-compliant data annotations.
For example, the efforts in setting up this new OMERO instance have enabled researchers at the CFCI to offer their original bioimaging data for reuse upon publication of the research project (see: Jannasch et al., (2024): In vivo application of a glutaraldehyde-free, UVA/riboflavin cross-linked bovine pericardium confirms suitability for cardiovascular substitutes. APL Mater. https://doi.org/10.1063/5.0182672).
The full report on setting up the new OMERO instance including detailed reports on the use cases is now available in the Journal of Microscopy:
Jannasch, A., Tulok, S., Okafornta, C. W., Kugel, T., Bortolomeazzi, M., Boissonnet, T., Schmidt, C., Vogelsang, A., Dittfeld, C., Tugtekin, S.-M., Matschke, K., Paliulis, L., Thomas, C., Lindemann, D., Fabig, G., & Müller-Reichert, T. (2024). Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users. Journal of Microscopy, 1–15. https://doi.org/10.1111/jmi.13360