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Next Generation File Formats for BioImaging


Project Open Microscopy Environment
Lead

Jason Swedlow (University of Dundee)

Funding Cycle 1

Proposal Summary

To support the Bio-Formats user community and develop new formats to make proprietary file formats obsolete.


Project

Open Microscopy Environment

Bio-Formats is a software tool for reading and writing image data using standardized, open formats. Bio-Formats is a community driven project with an API that supports open source analysis programs like ImageJ, CellProfiler, Icy, and R, and informatics solutions like OMERO. Bio-Formats also plugs into Matlab and is embedded in several commercial software applications (e.g., Columbus from PerkinElmer, Amira from ThermoFisher, Zen Black from Carl Zeiss). Bio-Formats reads metadata and binary data from >150 proprietary file formats storing data from wide field, confocal, multi-photon, TIRF, light sheet, electron, scanning probe and many other forms of microscopy, as well as high content screening, digital pathology and medical imaging (including 17 DICOM variants). Bio-Formats converts all these data formats to the OME Data Model. Bio-Formats converts data on the fly and is often used as a plug-in library, but can also convert files to OME-TIFF and validate OME-TIFF files.


Key Personnel

Jason Swedlow
David Gault
Sebastien Besson
Petr Walczysko
Jean-Marie Burel