"Management of Microscopy Image Data: An overview of OMERO, BioImage Archive and Image Data Resource" 2025 @ Uni Leipzig

Management of Microscopy Image Data: An overview of OMERO, BioImage Archive and Image Data Resource Dr Riccardo Massei Research Data Management (RDM) at UFZ – Workflows and Pipelines Expert Group Data Steward at NFDI4BIOIMAGE Uni Leipzig, RDM series 04/07/2025 These slides were created and adapted from the OMERO Training Material (https://zenodo.org/records/8323588) OMERO: An open-source software for image data management OMERO = „OME Remote Objects“ Created by the Open Microscopy Environment Consortium (OME) •User computer •Microscope computer •Processing / analysis server •Installed on an institute or central IT server •Storage and handling of imaging data •Accessible from outside via „clients“ https://zenodo.org/records/8323588) Slides_01: What is OMERO? From isolated data silos… https://zenodo.org/records/8323588) Slides_01: What is OMERO? … to centralized, structured data management https://zenodo.org/records/8323588) Slides_01: What is OMERO? Advantages of using OMERO •Organize your original image files in a central storage location •Unique IDs for images; data can be linked via IDs •View your images, add annotations, tags, and comments to your images •View & explore images, and adjust, save and share visualization settings •Create publication-ready figures connected to original image files •Export image data to different formats •Analyze image data •Built-in analysis functions •Connect to popular image analysis software like Fiji or QuPath •Share your data with colleagues •and more… https://zenodo.org/records/8323588) Slides_01: What is OMERO? Login into OMERO Service provided for researchers centrally by the RDM and IT Department Get your account & log in with your credentials Use OMERO •for yourself •with your group •with collaboration partners Enter your user name & password https://zenodo.org/records/8323588) Slides_02: Connect to OMERO Two ways of connecting to the OMERO server as a user „OMERO.insight“ client OR „OMERO.web“ client both clients offer similar functionalities Adapted from https://omero.readthedocs.io/en/latest/users/index.html More information on clients: https://omero.readthedocs.io/en/latest/users/clients-overview.html Desktop client •Installed by the user on a local computer •Recommended for: •Importing data into OMERO •Importing metadata Browser-based web-client •Installed by the IT department on the server, users access it with a browser •Recommended for: •Visualizing data •Analyzing and managing data •Annotating data (e.g., with tags) •Running scripts •It is not used to upload data! https://zenodo.org/records/8323588) Slides_02: Connect to OMERO Connecting with OMERO.web 1. Open an internet browser and enter the address of your OMERO server 2. Enter your username and password (usually the student/employee credentials) Be sure to connect -from the institute‘s network -via a VPN connection OMERO WEB SERVER ADDRESS 2.Enter username and password 1. Enter server address https://zenodo.org/records/8323588) Slides_02: Connect to OMERO OMERO.web overview example data Data tree Hierarchy: -user/group --project ---dataset ----image(s) Thumbnail preview of images in the dataset Tags & key value pairs Information on your data(set) and metadata User settings https://zenodo.org/records/8323588) Slides_03: OMERO explained File folder hierarchy in explorer vs object-based data structure A file folder hierarchy is itself a form of metadata OMERO uses structured metadata, e.g., with Tags and Key-Value Pairs https://zenodo.org/records/8323588) Slides_06: Data Organization example data How is metadata organized in OMERO? Metadata is contained: 1. In the data organization tree (implicitly) 2. Under the General tab •Image Details •Tags •Key-Value Pairs •Attachments •Ratings 3. Under the Acquisition tab: •Original metadata Metadata Tags and Key-Value Pairs 12 3 https://zenodo.org/records/8323588) Slides_06: Data Organization Tags •Tags allow a dynamic representation of the data tree •Data tree is re-arranged in Tag-based search according to the search interest •Tags can define similarities and relationships •Tags can be used to quickly access and process data of interest Examples (Tags): •„show all data for samples treated with compound A“ •„show all data for samples incubated for 3 h“ •„show all data recorded with instrument A“ •etc… Tags denote a specific property of an entity (like a price tag in the supermarket) https://zenodo.org/records/8323588) Slides_07-1: Metadata Tags Key-Value Pairs Consist of •Key: Denotes a real-world object or an abstract concept that can be assigned a specific value (of several or many possible values) •Value: Number or text string that specifies the object denoted under „Key“ Examples: Key: „cell type“ Value: „CD4+ T cell“ Key: „disease model“ Value: „experimental autoimmune encephalomyelitis“ Key-Value Pairs allow (standardized) annotation of detailed metadata https://zenodo.org/records/8323588) Slides_07-2: Metadata KeyValues Data visualization in OMERO OMERO.viewer OMERO.figures OMERO.tables Bio Image Archieve (BIA) and IDR BioImage Archive (BIA) A public repository for biological imaging data across modalities and scales. Hosted by EMBL-EBI (European Bioinformatics Institute) ●Supports many different imaging modalities ●Stores raw and processed data ●Accepts datasets from published studies or pre-prints ●Long-term data preservation ●Easy and well-documented dataset submission with metadata templates Image Data Repository (IDR) A curated, cloud-based resource for bioimaging data integration and reanalysis. Built on top of OMERO and hosted by EMBL-EBI. ●Focus on reference datasets with detailed experimental metadata. ●Rich annotations: phenotypes, gene functions, ontology terms. ●Supports high-content screening and large-scale imaging studies. Bio Image Archieve (BIA) and IDR RDM Guidelines: https://rdm.pages.ufz.de/guidelines/ Personal GitHub: https://github.com/rmassei Consult our Help Desk! https://nfdi4bioimage.de/help-desk [email protected] DaSt Team These slides were created and adapted from the OMERO Training Material (https://zenodo.org/records/8323588) Schmidt, C., Bortolomeazzi, M., Boissonnet, T., FortmannGrote, C., Dohle, J., Zentis, P., Kandpal, N., Kunis, S., Zobel, T., Weidtkamp-Peters, S., & Ferrando-May, E. (2023). I3D:bio's OMERO training material: Re-usable, adjustable, multipurpose slides for local user training. Zenodo.