Abstract
The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.
Highlights
Biological imaging is one of the most innovative fields in the modern biological sciences
While there is a strong drive to make scientific data findable, accessible, interoperable and reusable (FAIR1), the rapid rate of innovation in imaging has resulted in the creation of hundreds of proprietary file formats (PFFs) and has prevented the unification and adoption of standardized data formats
Open formats like OME-TIFF3 and HDF5 are often used for permanent conversion, but both have limitations that make them ill-suited for use cases that depend on very high and frequent levels of access, such as training of artificial intelligence models and publication of reference bioimage datasets in cloud-based resources
Summary
Biological imaging is one of the most innovative fields in the modern biological sciences. Licensed example datasets from the Image Data Resource (IDR)[10] have been converted into Zarr and stored in an S3-object storage bucket for public consumption (Extended Data Fig. 1).
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