# 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. ## Connections - Governed by: [[OME]] - Endorsed by: [[Euro-BioImaging]], [[ELIXIR]] - Metadata standards: [[REMBI]] ## Resources - https://www.openmicroscopy.org/ome-files/ (OME-TIFF) - https://ngff.openmicroscopy.org (OME-NGFF specification) - https://github.com/ome/ngff (community specification repository)