ngff-zarr

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A multi-language implementation of the Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr specification.

Repository Structure

This repository contains multiple packages implementing NGFF-Zarr support:

• py/ - Python package (ngff-zarr) - A lean and kind NGFF-Zarr implementation
• mcp/ - Model Context Protocol (MCP) server (ngff-zarr-mcp) for AI integration
• TypeScript package - Coming soon

Python Package (py/)

The main Python package provides:

✨ 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>=3.9
• Reads OME-Zarr v0.1 to v0.5 into simple Python data classes with Dask arrays
• Optional OME-Zarr data model validation during reading
• Writes OME-Zarr v0.4 to v0.5
• Sharded Zarr stores
• Optional writing via tensorstore

📖 Documentation

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

MCP Server (mcp/)

The Model Context Protocol server enables AI assistants like Claude to interact with NGFF-Zarr files. See the MCP documentation for setup and usage instructions.

See also

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

License

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