OME-Zarr: a cloud-optimized bioimaging file format with international community support

Abstract

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

The Brain Image Library: A Community-Contributed Microscopy Resource for Neuroscientists

“…Most deposited images are volumetric stacks in native TIFF and JPEG 2000 image file formats. Currently, we are encouraging the use of high-performance next-generation file formats (NGFF) 16 such as multiscale OME-Zarr 17 , which represent multi-resolution image pyramids optimized for rapid visualization and scalable analysis. While BIL continues to accommodate historically accepted file formats, datasets in these formats may not fully leverage the complete range of visualization capabilities now provided through BIL.…”

“…For datasets that have not yet been submitted to BIL, we are encouraging data providers to submit datasets that can be easily converted to OME-Zarr or provide data in a format that is compatible with our on-demand transformer for direct access in OME-Zarr. More information on the on-demand transformer and our plan to serve OME-Zarr dynamically at BIL can be found in the paper describing community adoption of OME-Zarr 17 . We plan to detail the capabilities of the on-demand transformer in a separate publication.…”

HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression

“…automatically generated by the microscope and saved in separated XML files. While this second mechanism is currently only implemented for the CellVoyager format from Yokogawa and for imaging datasets generated by Micro-Manager, the open source and modular nature of HiTIPS allows the future extension of metadata reading from files to other instruments and formats, potentially including the recently developed OMERO-ZARR format 20 . Thanks to the use of image acquisition metadata by HiTIPS, users can select specific wells, FOVs, and/or channels to quickly load single merged FOVs in the viewer for visual inspection and for optimization of the image analysis parameters (Fig.…”

Mantis: high-throughput 4D imaging and analysis of the molecular and physical architecture of cells

“…The acquired multidimensional raw datasets are processed by the shrimPy reconstruction engine to generate registered multimodal data that can be used for analysis (Figure 2a). Raw data are first converted into the OME-Zarr format (31), which enables efficient parallel processing of multiple timepoints and positions. As described below, discrete data volumes then undergo deskewing of fluorescence channels, reconstruction of phase and orientation, registration and virtual staining.…”