ngff-zarr0.20.0
ngff-zarr0.20.0
Published
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
pip install ngff-zarr
Package Downloads
Authors
Project URLs
Requires Python
>=3.9
Dependencies
- dask
[array] - importlib-resources
- itkwasm-downsample
>=1.8.0 - itkwasm
>=1.0b183 - numpy
- platformdirs
- psutil
; sys_platform != "emscripten" - rich
- rich-argparse
- typing-extensions
- zarr
- dask-image
; extra == "all" - dask
[distributed]; extra == "all" - deepdiff
; extra == "all" - furo
<2025,>=2024.7.18; extra == "all" - imagecodecs
; extra == "all" - imageio
; extra == "all" - itk-filtering
>=5.3.0; extra == "all" - itk-io
>=5.3.0; extra == "all" - itkwasm-image-io
; extra == "all" - jsonschema
; extra == "all" - myst-parser
<4,>=3.0.1; extra == "all" - nibabel
; extra == "all" - pooch
; extra == "all" - pytest
>=6; extra == "all" - sphinx-autobuild
<2025,>=2024.4.16; extra == "all" - sphinx-autodoc2
<0.6,>=0.5.0; extra == "all" - sphinx-copybutton
<0.6,>=0.5.2; extra == "all" - sphinx-design
<0.7,>=0.6.0; extra == "all" - sphinx
<8,>=7.4.7; extra == "all" - sphinxext-opengraph
<0.10,>=0.9.1; extra == "all" - tensorstore
; extra == "all" - tifffile
>=2024.7.24; extra == "all" - dask-image
; extra == "cli" - dask
[distributed]; extra == "cli" - imagecodecs
; extra == "cli" - imageio
; extra == "cli" - itk-filtering
>=5.3.0; extra == "cli" - itk-io
>=5.3.0; extra == "cli" - itkwasm-image-io
; extra == "cli" - nibabel
; extra == "cli" - tifffile
>=2024.7.24; extra == "cli" - dask-image
; extra == "dask-image" - furo
<2025,>=2024.7.18; extra == "docs" - myst-parser
<4,>=3.0.1; extra == "docs" - sphinx-autobuild
<2025,>=2024.4.16; extra == "docs" - sphinx-autodoc2
<0.6,>=0.5.0; extra == "docs" - sphinx-copybutton
<0.6,>=0.5.2; extra == "docs" - sphinx-design
<0.7,>=0.6.0; extra == "docs" - sphinx
<8,>=7.4.7; extra == "docs" - sphinxext-opengraph
<0.10,>=0.9.1; extra == "docs" - itk-filtering
>=5.3.0; extra == "itk" - tensorstore
; extra == "tensorstore" - deepdiff
; extra == "test" - pooch
; extra == "test" - pytest
>=6; extra == "test" - jsonschema
; extra == "validate"
ngff-zarr
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>=3.9
- 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 on command line usage, the Python API, library features, and how to contribute can be found in our documentation.
See also
License
ngff-zarr is distributed under the terms of the
MIT license.