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OME File Formats — OME-TIFF and OME-NGFF (OME-Zarr)

Overview

The OME file formats are the open standards for storing and sharing biological microscopy image data, produced by the OME consortium. There are two complementary formats covering different use cases: OME-TIFF for stable archival and publication, and OME-Zarr (OME-NGFF) for large-scale, cloud-native analysis.

OME-TIFF

The established standard, combining the widely-supported TIFF image format with embedded OME-XML metadata in the image header.

  • It embeds rich structured metadata (acquisition parameters, instrument, channels, specimen, experimenter) directly within the TIFF file.
  • It supports multi-dimensional data including Z-stacks, time series, multichannel images, and tiled large images.
  • Pyramidal multi-resolution support enables whole-slide imaging.
  • It is produced from proprietary formats via Bio-Formats, the OME conversion library.
  • It is the required format for deposition to the BioImage Archive and IDR (Image Data Resource at EMBL-EBI).
  • It is widely supported by ImageJ/Fiji, QuPath, CellProfiler, OMERO, and napari.

OME-NGFF (OME-Zarr)

The next-generation format, designed for cloud storage, streaming access, and very large multidimensional datasets (terabyte-scale light-sheet, expansion microscopy, and whole-brain imaging).

  • It is based on Zarr, a chunked and compressed array format enabling random access to any region without downloading the full file.
  • It is cloud-native, reading directly from S3, Google Cloud Storage, or HTTP.
  • It supports multi-resolution pyramids for progressive rendering.
  • It uses a separate community metadata specification (the OME-NGFF spec, versioned openly).
  • It is increasingly adopted by Euro-BioImaging nodes and the BioImage Archive.

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