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Bioimage analysis for research data management

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posted on 2023-03-03, 14:16 authored by Tom BoissonnetTom Boissonnet, Julia Dohle, Tobias Wernet, Christian Schmidt, Karen Bernhardt, Susanne Kunis, Josh MooreJosh Moore, Roland Nitschke, Stefanie Weidtkamp-Peters, Elisa Ferrando-May

Poster presented as part of the Crick BioImage Analysis Symposium.

Microscopy data size, quantity, and acquisition techniques are growing at remarkable rates. At the same time, research data management (RDM) practices lag behind: data is stored on personal computers and external hard drives, data is sparsely annotated and experimental metadata is often not linked. In addition, the specificity of research fields hampers the search for standards. In response, multiple initiatives have emerged. Ours, named I3D:bio (Information Infrastructure for BioImage Data,, aims to facilitate the deployment of OMERO [1] servers, the most popular solution for the management of microscopy images [2]. Thus, our purpose is to generalize the availability of OMERO so to expose more researchers to OMERO, while producing clear RDM guidelines and user documentation for integrating analysis software. These will help users to connect many popular image analysis tools (ImageJ, CellProfiler, napari, ilastik, QuPath) with their OMERO servers, demonstrating the usefulness of annotated data. Our goal is therefore to promote OMERO as an endpoint for image analysis and encourage more image analysis tools to interoperate with OMERO. By proposing more workflows around OMERO, we hope to obtain a faster adoption of RDM by researchers. 

Permission has been given by authors to upload to Crick Figshare. Copyright remains with the original holders.  


I3D:bio - Information Infrastructure for BioImage Data

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