https://github.com/thewtex/ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
https://github.com/thewtex/ngff-zarr

dask imaging medical microscopy ome-zarr ome-zarr-converter python

Last synced: about 1 year ago
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A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

• Host: GitHub
• URL: https://github.com/thewtex/ngff-zarr
• Owner: thewtex
• License: mit
• Created: 2022-09-27T00:37:16.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2025-02-20T21:38:39.000Z (over 1 year ago)
• Last Synced: 2025-03-31T04:05:12.507Z (about 1 year ago)
• Topics: dask, imaging, medical, microscopy, ome-zarr, ome-zarr-converter, python
• Language: Python
• Homepage: https://ngff-zarr.readthedocs.io
• Size: 702 KB
• Stars: 32
• Watchers: 4
• Forks: 7
• Open Issues: 18
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# ngff-zarr

[![PyPI - Version](https://img.shields.io/pypi/v/ngff-zarr.svg)](https://pypi.org/project/ngff-zarr)

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---

A lean and kind

[Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr](https://ngff.openmicroscopy.org)

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>=3.9

- 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

- Optional writing via [tensorstore](https://google.github.io/tensorstore/)

## Documentation

More information an command line usage, the Python API, library features, and

how to contribute can be found in

[our documentation](https://ngff-zarr.readthedocs.io/).

## See also

- [ome-zarr-py](https://github.com/ome/ome-zarr-py)

- [multiscale-spatial-image](https://github.com/spatial-image/multiscale-spatial-image)

- [itk-ioomezarrngff](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF)

- [iohub](https://czbiohub-sf.github.io/iohub/)

- [pydantic-ome-ngff](https://janeliascicomp.github.io/pydantic-ome-ngff/)

- [aicsimageio](https://allencellmodeling.github.io/aicsimageio/)

- [bfio](https://bfio.readthedocs.io/)

## License

`ngff-zarr` is distributed under the terms of the

[MIT](https://spdx.org/licenses/MIT.html) license.