Completed Plants, Animals & Ecology Cells, Biochemistry & Physiology

OME's Bio-Formats: Tools for Next Generation Image Data & Metadata Access

Funder Wellcome Charity-funded
Recipient organisation University of Dundee
Funding £1.4M
Period Oct 2016 — Sept 2019

In plain English

AI plain-English summary

A single software library, Bio-Formats, already lets scientists read biological image data from hundreds of proprietary file formats and convert it into a common, open standard. This matters because biological imaging—from microscopes to high-throughput screens—generates data in dozens of incompatible proprietary formats. Without tools like Bio-Formats, researchers waste time converting files or risk losing access to data locked in obsolete formats. The project fills a gap in data interoperability: it provides a universal translator for scientific images, ensuring that data can be reused, shared, and analysed regardless of the original instrument or software. If successful, the proposed updates will allow Bio-Formats to handle much larger datasets—such as tiled, multi-resolution images and 3D volumes—and to save and retrieve data from cloud object stores. It will also extend metadata support to include tabular data from spreadsheets and HDF5 files. These improvements will make it easier for labs worldwide to manage, share, and analyse ever-growing image datasets, and will underpin public image repositories that serve the entire research community. The impact is on the infrastructure of biological research itself: faster, more reliable access to the raw data that drives discovery.

View original technical description
Since 2000, the Open Microscopy Environment (OME) has built open source interoperability tools for biological image data. The project has three components: • OME Data Model, a metadata specification for biological imaging; • Bio-Formats, a suite of libraries available in Java and C++, for reading proprietary scientific image data and metadata into a common model, available to any 3rd party software; • OMERO, a client-server software platform for image data management and analysis. OME’s tools enable access to data, regardless of storage format, programming environment, or geographical location. They are used in 1000s of academic and industrial labs worldwide and are the foundation for several public on-line image repositories. Our proposed aims are deliberately chosen to extend the reach and utility of Bio-Formats. We will: 1. Update Bio-Formats architecture to support: i. faster access and rendering of larger datasets, and in particular tiled, multi-resolution pyramids and 3D volumes, and hyperspectral images ii. saving and accessing data in object stores, i.e., Amazon S3 2. Extend the range of metadata supported by OME’s software, releasing an “OME Files” software suite that reads and writes experimental and analytic metadata from tabular data sources (i.e., spreadsheet and HDF5 files)

View the original record at the funder ↗

Researchers

Jason Swedlow (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

Expanded Metadata Support in the Open Microscopy Environment's Bio-Formats & OMERO Data Applications
The Open Microscopy Environment: towards the development of a scientific data management system.
New Open File Formats for the Biological Imaging Community
Open image informatics software for biological microscopy
Implementation of LSIDs in the Open Microscopy Environment

Original classification

Biomedical Resources Grant

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