Microscopy and bioimaging technologies are fundamental tools for exploring biological systems, generating large, multidimensional datasets rich in experimental detail. However, the bioimaging community has historically faced major challenges around data handling: vendor-specific proprietary formats, fragmented metadata storage, and increasingly large dataset sizes that outstrip traditional storage and computing solutions.

In this webinar, we will present key open technologies developed by the Open Microscopy Environment (OME) to address these challenges. Specifically, we will introduce the Bio-Formats library for accessing diverse proprietary file formats, the OME-TIFF standard for archival data storage, and the OME-Zarr format for cloud-native, scalable bioimaging workflows. We will show how these technologies can be used to:

• Read and standardise imaging datasets from hundreds of proprietary file formats
• Store data and metadata together in accessible, interoperable formats
• Enable scalable storage and analysis of large, multidimensional imaging datasets using modern cloud and cluster environments
• Improve data sharing and reproducibility in line with FAIR (Findable, Accessible, Interoperable, Reusable) principles

Who is this course for?

This webinar is suitable for any researcher, data manager, or imaging specialist working with microscopy data who is interested in improving data accessibility, interoperability, and scalability. No prior experience with file formats or image data standards is required, but an undergraduate level understanding of biological imaging concepts will be useful.

This event is part of a webinar series organised by the STANDFLOW project, an initiative supported by EMBL’s Planetary biology Transversal Theme. STANDFLOW is about a collaborative effort towards creating a standardised data management workflow. The project primarily utilises imaging data derived from samples collected through the TREC (Traversing European Coastlines) and the Roscoff Culture Collection. For details on all topics covered in this series and registration information, please visit the following link: How to organise and share my imaging data?: Multimodal data management for marine biologists, and environmental scientists and imaging specialists. 

Outcomes

By the end of the webinar, you will be able to:

• Describe the challenges posed by proprietary bioimaging file formats and large datasets
• Explain the purpose and capabilities of Bio-Formats, OME-TIFF, and OME-Zarr
• Identify strategies for reading, converting, storing, and sharing bioimaging datasets in open formats
• Discuss how open standards contribute to building scalable, interoperable, and FAIR imaging workflows

DOI: 10.6019/TOL.OMEBioFormats-w.2025.00001.1

This webinar took place on 21 May 2025. Please click the 'Watch video' button to view the recording.