ngff-zarr
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
MIT License
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What's Changed
- ENH: Bump itkwasm-downsample to support more label image types by @thewtex in https://github.com/thewtex/ngff-zarr/pull/74
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.8.1...v0.8.2
Published by thewtex 8 months ago
What's Changed
- BUG: Detect .ome.zarr as supported by NGFF_ZARR by @thewtex in https://github.com/thewtex/ngff-zarr/pull/73
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.8.0...v0.8.1
Published by thewtex 8 months ago
What's Changed
- DOC: Document CUDA acceleration by @thewtex in https://github.com/thewtex/ngff-zarr/pull/68
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.7.0...v0.8.0
Published by thewtex 9 months ago
What's Changed
- DOC: myst, autodoc2 supported formatting for to_multiscales, to_ngff_… by @thewtex in https://github.com/thewtex/ngff-zarr/pull/62
- BUG: Pass correct kwarg to LocalCluster for memory_limit by @thewtex in https://github.com/thewtex/ngff-zarr/pull/63
- DOC: Format to_ngff_zarr for myst / autodoc2 by @thewtex in https://github.com/thewtex/ngff-zarr/pull/64
- Itkwasm downsample by @thewtex in https://github.com/thewtex/ngff-zarr/pull/61
- ENH: Default method is ITKWASM_GAUSSIAN by @thewtex in https://github.com/thewtex/ngff-zarr/pull/65
- DOC: Add some documentation for current methods by @thewtex in https://github.com/thewtex/ngff-zarr/pull/66
- Cli io wasm by @thewtex in https://github.com/thewtex/ngff-zarr/pull/67
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.6.0...v0.7.0
Published by thewtex 11 months ago
What's Changed
- NGFF Schema validation by @thewtex in https://github.com/thewtex/ngff-zarr/pull/7
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.5.0...v0.6.0
Published by thewtex 11 months ago
What's Changed
- Sigma by @thewtex in https://github.com/thewtex/ngff-zarr/pull/56
- ENH: Clean up scale cache stores before process exit by @thewtex in https://github.com/thewtex/ngff-zarr/pull/57
- BUG: Support reading and writing an OME-Zarr created by omero-zarr by @thewtex in https://github.com/thewtex/ngff-zarr/pull/58
- BUG: Reset image.computed_callbacks after calling by @thewtex in https://github.com/thewtex/ngff-zarr/pull/59
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.7...v0.5.0
Published by thewtex about 1 year ago
What's Changed
- BUG: Support dim dict scale factors in _downsample_dask_image by @thewtex in https://github.com/thewtex/ngff-zarr/pull/51
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.6...v0.4.7
Published by thewtex about 1 year ago
What's Changed
- More dimension_separator="/" added, so napari can open big data as well by @GFleishman in https://github.com/thewtex/ngff-zarr/pull/47
- nested separator in to_ngff_zarr, fixed napari display problem by @GFleishman in https://github.com/thewtex/ngff-zarr/pull/46
- Scipy py cookie by @thewtex in https://github.com/thewtex/ngff-zarr/pull/50
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.5...v0.4.6
Published by thewtex over 1 year ago
What's Changed
- absolute vs. relative scales bug fix in _dim_scale_factors by @GFleishman in https://github.com/thewtex/ngff-zarr/pull/41
- DOC: Factor README docs into Sphinx by @thewtex in https://github.com/thewtex/ngff-zarr/pull/43
- ENH: Add imagecodecs as a cli dependency by @thewtex in https://github.com/thewtex/ngff-zarr/pull/42
New Contributors
- @GFleishman made their first contribution in https://github.com/thewtex/ngff-zarr/pull/41
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.4...v0.4.5
Published by thewtex over 1 year ago
What's Changed
- BUG: Set units dictionary from CLI instead of updating existing by @tbirdso in https://github.com/thewtex/ngff-zarr/pull/36
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.3...v0.4.4
Published by thewtex over 1 year ago
What's Changed
- BUG: Do not break task graph for first level by @thewtex in https://github.com/thewtex/ngff-zarr/pull/35
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.2...v0.4.3
Published by thewtex over 1 year ago
What's Changed
- BUG: Scale propagation fix by @tbirdso in https://github.com/thewtex/ngff-zarr/pull/30
- BUG: Store zarr array regions when caching slabs by @thewtex in https://github.com/thewtex/ngff-zarr/pull/34
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.1...v0.4.2
Published by thewtex over 1 year ago
What's Changed
- ENH: Add support for setting axis units from CLI by @tbirdso in https://github.com/thewtex/ngff-zarr/pull/24
- BUG: Relax expectation of '@type' when reading other store metadata by @thewtex in https://github.com/thewtex/ngff-zarr/pull/31
New Contributors
- @tbirdso made their first contribution in https://github.com/thewtex/ngff-zarr/pull/24
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.4.0...v0.4.1
Published by thewtex over 1 year ago
What's Changed
- ENH: Add ngff_image_to_itk_image by @thewtex in https://github.com/thewtex/ngff-zarr/pull/26
- Large write by @thewtex in https://github.com/thewtex/ngff-zarr/pull/25
- DOC: Add OME-Zarr spec version to README by @thewtex in https://github.com/thewtex/ngff-zarr/pull/27
- Vector image by @thewtex in https://github.com/thewtex/ngff-zarr/pull/29
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.3.0...v0.4.0
Published by thewtex over 1 year ago
What's Changed
- Itk backend by @thewtex in https://github.com/thewtex/ngff-zarr/pull/13
- ENH: Support for larger-than-memory volumes, CLI by @thewtex in https://github.com/thewtex/ngff-zarr/pull/15
- Large tiff by @thewtex in https://github.com/thewtex/ngff-zarr/pull/16
- ENH: Test Python 3.11 in CI by @thewtex in https://github.com/thewtex/ngff-zarr/pull/18
- Live output by @thewtex in https://github.com/thewtex/ngff-zarr/pull/19
- BUG: Do not use progress callbacks with distributed scheduler by @thewtex in https://github.com/thewtex/ngff-zarr/pull/20
- More docs by @thewtex in https://github.com/thewtex/ngff-zarr/pull/21
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.2.0...v0.3.0
Published by thewtex over 1 year ago
What's Changed
- BUG: Support multicomponent itk image conversion by @thewtex in https://github.com/thewtex/ngff-zarr/pull/9
- Downscale factors by @thewtex in https://github.com/thewtex/ngff-zarr/pull/11
- ENH: Add itk.VectorImage support by @thewtex in https://github.com/thewtex/ngff-zarr/pull/12
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.1.5...v0.2.0
Published by thewtex almost 2 years ago
What's Changed
- Nil chunks by @thewtex in https://github.com/thewtex/ngff-zarr/pull/8
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.1.4...v0.1.5
Published by thewtex almost 2 years ago
What's Changed
- BUG: Do not add another scale after min_length scale_factor reached by @thewtex in https://github.com/thewtex/ngff-zarr/pull/6
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.1.2...v0.1.4
Published by thewtex about 2 years ago
What's Changed
- BUG: Dask dictionary for aligned chunks when rechunking by @thewtex in https://github.com/thewtex/ngff-zarr/pull/4
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.1.1...v0.1.2
Published by thewtex about 2 years ago
What's Changed
- Ci by @thewtex in https://github.com/thewtex/ngff-zarr/pull/3
New Contributors
- @thewtex made their first contribution in https://github.com/thewtex/ngff-zarr/pull/3
Full Changelog: https://github.com/thewtex/ngff-zarr/compare/v0.1.0...v0.1.1
