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ngff zarr 0.5 #284

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Dec 11, 2024
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ngff zarr 0.5 #284

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4e97752
tools: note that File Reading/Writing tools also support conversion
thewtex Dec 9, 2024
37d0e2a
rfc-2: note ngff-zarr implementation support
thewtex Dec 9, 2024
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12 changes: 12 additions & 0 deletions rfc/2/index.md
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Expand Up @@ -287,6 +287,18 @@ See [Background](#background) for a list of v3-capable Zarr libraries.

Support for the OME-Zarr 0.5 metadata is under development in [ome-zarr-py](https://github.com/ome/ome-zarr-py/pull/383/files) and other implementations.

[ngff-zarr](https://ngff-zarr.readthedocs.io/) supports creating [OME-Zarr 0.5
from
Python](https://ngff-zarr.readthedocs.io/en/latest/python.html#array-to-ngff-image)
via Zarr-Python or
[Tensorstore](https://ngff-zarr.readthedocs.io/en/latest/python.html#writing-with-tensorstore),
[converting
OME-Zarr](https://ngff-zarr.readthedocs.io/en/latest/python.html#convert-ome-zarr-versions)
version 0.4 to 0.5 and 0.5 to 0.4, [validating OME-Zarr 0.5
metadata](https://ngff-zarr.readthedocs.io/en/latest/python.html#validate-ome-zarr-metadata),
and [converting other file formats to OME-Zarr
0.5](https://ngff-zarr.readthedocs.io/en/latest/cli.html).

## Drawbacks, risks, alternatives, and unknowns

While it is clear that Zarr v3 will become the predominant version of the specification moving forward, current library support for v3 is still under active development.
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5 changes: 4 additions & 1 deletion tools/index.md
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Expand Up @@ -17,6 +17,9 @@ In addition to this collection, an evaluation of selected tools/libraries is ava
| AICS Image Viewer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/allen-cell-animated/website-3d-cell-viewer) | A browser-based volume viewer built with React and WebGL (Three.js). |

## File Conversion

Many of the tools in the *File Reading/Writing* section below also support format conversion.

| Name | Link | Description |
| -------- | ------- | ------- |
| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. |
Expand Down Expand Up @@ -45,4 +48,4 @@ Various libraries for reading/writing OME-Zarr files in Python were evaluated as
| Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. |
| ome-ngff-validator | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-ngff-validator) | Web page for validating OME-NGFF files. |
| SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. |
| tensorstore | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/google/tensorstore/) | Library for reading and writing large multi-dimensional arrays (e.g., Zarr). |
| tensorstore | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/google/tensorstore/) | Library for reading and writing large multi-dimensional arrays (e.g., Zarr). |
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