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@fideus-labs/ngff-zarr

v0.2.0

Published

TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files

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Links

Git

Maintainers

thewtexthewtex

Keywords

ome-zarrzarrmicroscopyimagingngfftypescriptdeno

Readme

ngff-zarr

PyPI - Version PyPI - Python Version Python CI Testing Typescript CI Testing MCP CI Testing DOI Documentation Status

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 zarr-python 2, zarr-python 3, tensorstore or zarrita (TypeScript)
  • 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.

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

License

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