Workshop Research Data Management for Microscopy at University Münster

Research Data Management for Microscopy OMERO basics Jens Wendt With the exception of logos and cited third-party content, the content of these slides is shared under the terms of the Creative Commons Attribution License (CC-BY 4.0)unless the content is marked otherwise. Research Data Management for Microscopy Where do you come from, where do you go? … 1 - Developed by small developer team of OME (Open Microscopy Environment) in Dundee, Ireland - 12+ years old - Strong emphasis on community integration →everyone can request features/report issues →everyone can contribute to the code - Continuing development, improvement and integration with more/new tools/technologies (ome-zarr, S3, CellProfiler,…) Research Data Management for Microscopy I would do anything for [image data]… …but I won’t do that 2 •Store/archive your image data with its metadata (in the cloud) •Provide access to your data from anywhere, anytime •Provide an easy solution to share your image data with externals •Visualize your images •Publish your data out of OMERO •Provide an interface/integration with other (image analysis) tools •Analyze your images •Provide a detailed, quick Viewer, or even a 3D Viewer Research Data Management for Microscopy Technically … 3 - OMERO Server lives on a virtual machine in the University cloud - Image data is stored on a NFS FileShare (similar to UserShare) inaccessible from the outside →NOT a free of charge freely accessible storage space in the Uni Cloud (→UserShare) - Web-based frontend →GUI only reachable via the browser - Desktop application OMERO.insight only used for image upload Research Data Management for Microscopy What makes OMERO so appealing? 4 - Core credo: Your raw image data will not get changed in any way, ever! - Uses BioFormats - Developed by the same team of OME - Can read 150+ image file formats -Is the “black box” working its magic for ImageJ/Fiji, QuPath, etc. - Open source, with a big community essentially acting like a giant help desk on Image.sc - No data lock / living data Research Data Management for Microscopy The basic details 5 - How do I reach the website? →omero-imaging.uni-muenster.de (no need for VPN) - How do I log in? →with your University login - How do I get into a group? →contact us (Mattermost (Team “Imaging Network”), Email [email protected]) Research Data Management for Microscopy The web interface 6 Research Data Management for Microscopy Data structure 7 - Projects, Datasets, Images - Screens, Plates, Wells, Images →No endless subfolders possible Research Data Management for Microscopy The Viewer 8 - No 3D visualization - Very rudimentary: Brightness & Contrast, LUTs - Can create ROIs - Maximum Intensity Projection possible Research Data Management for Microscopy Acknowledgments Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrasstructure – NFDI 46/1 –501864659 The NFDI4BIOIMAGE consortium comprises legally independent partners and does not act autonomously towards third parties. The authors represent the contributions from their respective affiliated institutions and work together for the project.