ngff-zarr

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A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

✨ Features

• Minimal dependencies
• Work with arbitrary Zarr store types
• Lazy, parallel, and web ready -- no local filesystem required
• Process extremely large datasets
• Conversion of most bioimaging file formats
• Multiple downscaling methods
• Supports Python>=3.11
• Reads OME-Zarr v0.1 to v0.6 into simple Python data classes with Dask arrays
• Optional OME-Zarr data model validation during reading
• Writes OME-Zarr v0.4 to v0.6
• v0.6 adds RFC-5 coordinate systems and transformations
• Sharded Zarr stores
• Zarr I/O backed by zarrista / Rust zarrs (Python) or zarrita (TypeScript) -- no zarr-python dependency; OME-Zarr 0.4 (Zarr v2) outputs stay readable by zarr-python 2 and 3, and 0.5+ (Zarr v3) by zarr-python 3
• Anatomical orientation metadata (RFC-4)
• OME-Zarr Zip (.ozx) file support for single-file OME-Zarr datasets (RFC-9)
• High Content Screening (HCS) support for plate and well data
• Model Context Protocol (MCP) server for AI agent integration

Documentation

More information about command line usage, the Python API, library features, and how to contribute can be found in our documentation.

See also

• ome-zarr-py
• multiscale-spatial-image
• itk-ioomezarrngff
• iohub
• pydantic-ome-ngff
• aicsimageio
• bfio
• zod-ome-ngff

License

ngff-zarr is distributed under the terms of the MIT license.