What is OMERO?
OMERO is a free client-server platform for the management of image data. Developed by the University of Dundee and OME, OMERO has also been available at Osnabrück University since 2016. In the Biology department the repository now contains over 350 TB of data (as of May 2025).
From microscope to publication, OMERO manages all your image data on a secure, central server with a database for metadata. Over 150 image file formats are supported, including all major microscope formats.
You can view, organize, annotate, analyze and share your image data from anywhere with Internet access. Work with your images via a desktop application, the internet or via third-party software.
Further information can be found on the OMERO homepage.
- Data import/export
- Data analysis
- Data sharing (collaboration)
- Data publication
- Organizing and annotating data
- Searching and filtering data
More video tutorials can be found under I3D:bio's OMERO Training Videos (YouTube).
Schmidt, C., Boissonnet, T., Dohle, J., Bernhardt, K., Ferrando-May, E., Wernet, T., Nitschke, R., Kunis, S., & Weidtkamp-Peters, S. (2024). A practical guide to bioimaging research data management in core facilities. Journal of microscopy, 294(3), 350-371. https://doi.org/10.1111/jmi.13317
Kunis, S., Bernhardt, K., & Hensel, M. (2023). Setting up a data management infrastructure for bioimaging. Biological chemistry, 404(5), 433-439. https://doi.org/10.1515/hsz-2022-0304
Schmidt, C., Hanne, J., Moore, J., Meesters, C., Ferrando-May, E., Weidtkamp-Peters, S., & members of the NFDI4BIOIMAGE initiative (2022). Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey. F1000Research, 11, 638. https://doi.org/10.12688/f1000research.121714.2
Pouchin, P., Zoghlami, R., Valarcher, R., Delannoy, M., Carvalho, M., Belle, C., Mongy, M., Desset, S., & Brau, F. (2022). Easing batch image processing from OMERO: a new toolbox for ImageJ. F1000Research, 11, 392. https://doi.org/10.12688/f1000research.110385.2
Scherr, T., Seiffarth, J., Wollenhaupt, B., Neumann, O., Schilling, M. P., Kohlheyer, D., Scharr, H., Nöh, K., & Mikut, R. (2022). microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation. PloS one, 17(11), e0277601. https://doi.org/10.1371/journal.pone.0277601
Li, S., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gillen, K., Leigh, R., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Rustici, G., Tarkowska, A., Walczysko, P., Williams, E., Allan, C., Burel, J. M., Moore, J., ... Swedlow, J. R. (2016). Metadata management for high content screening in OMERO. Methods (San Diego, Calif.), 96, 27-32. https://doi.org/10.1016/j.ymeth.2015.10.006
Burel, J. M., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gillen, K., Leigh, R., Li, S., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Tarkowska, A., Walczysko, P., Allan, C., Moore, J., & Swedlow, J. R. (2015). Publishing and sharing multi-dimensional image data with OMERO. Mammalian genome : official journal of the International Mammalian Genome Society, 26(9-10), 441-447. https://doi.org/10.1007/s00335-015-9587-6
Allan, C., Burel, J. M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., Macdonald, D., Moore, W. J., Neves, C., Patterson, A., Porter, M., Tarkowska, A., Loranger, B., Avondo, J., Lagerstedt, I., Lianas, L., Leo, S., Hands, K., Hay, R. T., Patwardhan, A., ... Swedlow, J. R. (2012). OMERO: flexible, model-driven data management for experimental biology. Nature methods, 9(3), 245-253. https://doi.org/10.1038/nmeth.1896
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