Update yaozarrs' org

Author: lubianat

resources/tools/index.md

@@ -22,26 +22,26 @@ Want to view a Zarr? Use one of these.
 
 [Check this out](https://ome.github.io/ome-ngff-tools/) to see viewer compatibility with various OME-Zarr features & versions.
 
-| Name    | Link | Description | 
+| Name    | Link | Description |
 | -------- | ------- | ------- |
-| AGAVE | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org" alt="AGAVE logo" width="30" height="30">](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | 
+| AGAVE | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org" alt="AGAVE logo" width="30" height="30">](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU |
 | FIJI (MoBIE / BigDataViewer) | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://fiji.sc/" alt="FIJI logo" width="30" height="30">](https://mobie.github.io/) | [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data |
 | FIJI (n5-ij) | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://fiji.sc/" alt="FIJI logo" width="30" height="30">](https://github.com/saalfeldlab/n5-ij) | [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API |
 | ITKWidgets | [<img src="https://raw.githubusercontent.com/InsightSoftwareConsortium/itkwidgets/main/docs/_static/itkwidgets_logo.png" alt="ITKWidgets logo" width="30" height="30">](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) |
-| Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | 
-| napari | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://napari.org/" alt="napari logo" width="30" height="30">](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | 
-| Neuroglancer | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://google.com" alt="Neuroglancer logo" width="30" height="30">](https://github.com/google/neuroglancer) | A browser-based volume viewer | 
-| Viv (Avivator, Vizarr, Vitessce, ...) | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://vitessce.io/" alt="Viv logo" width="30" height="30">](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | 
-| Vol-E | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org%2Fpathtrace-rendering.html" alt="Vol-E logo" width="30" height="30">](https://vole.allencell.org/) | A browser-based volume viewer | 
-| WEBKNOSSOS | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://home.webknossos.org/" alt="WEBKNOSSOS logo" width="30" height="30">](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | 
+| Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data |
+| napari | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://napari.org/" alt="napari logo" width="30" height="30">](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr |
+| Neuroglancer | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://google.com" alt="Neuroglancer logo" width="30" height="30">](https://github.com/google/neuroglancer) | A browser-based volume viewer |
+| Viv (Avivator, Vizarr, Vitessce, ...) | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://vitessce.io/" alt="Viv logo" width="30" height="30">](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others |
+| Vol-E | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org%2Fpathtrace-rendering.html" alt="Vol-E logo" width="30" height="30">](https://vole.allencell.org/) | A browser-based volume viewer |
+| WEBKNOSSOS | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://home.webknossos.org/" alt="WEBKNOSSOS logo" width="30" height="30">](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets |
 
 
 ### Zarr converters (with a UI)
 
 Want to convert your file to Zarr? Use one of these tools that has a user interface.
 
-| Name    | Link | Description | 
-| -------- | ------- | ------- | 
+| Name    | Link | Description |
+| -------- | ------- | ------- |
 | NGFF-Converter | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/NGFF-Converter) | A desktop application for conversion of bioimage formats into OME-Zarr or OME-TIFF. |
 
 ## Tools for the programmatically inclined
@@ -54,14 +54,14 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi
 
 | Name    | Link | Description |
 | -------- | ------- | ------- |
-| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | 
-| 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-Zarr specification. | 
-| BioIO Conversion | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org" alt="BioIO logo" width="30" height="30">](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr)  |  
-| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. |  
-| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | 
-| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | 
+| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. |
+| 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-Zarr specification. |
+| BioIO Conversion | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org" alt="BioIO logo" width="30" height="30">](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr)  |
+| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. |
+| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing |
+| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing |
 | Nextflow (nf-omezarr) | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://www.nextflow.io/g" alt="Nextflow logo" width="30" height="30">](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw |
-| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. |  
+| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. |
 | stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. |
 | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. |
 
@@ -71,14 +71,14 @@ Want to read or write a Zarr? Use one of these tools.
 
 [Check this out](https://github.com/jwindhager/ome-ngff-readers-writers/) to see reader/writer compatibility with various OME-Zarr features & versions.
 
-| Name    | Link | Description | 
+| Name    | Link | Description |
 | -------- | ------- | ------- |
-| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | 
-| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | 
-| BioIO | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org" alt="BioIO logo" width="30" height="30">](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio))  | 
-| iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | 
-| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | 
-| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/thewtex/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | 
+| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. |
+| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) |
+| BioIO | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https%3A%2F%2Fwww.allencell.org" alt="BioIO logo" width="30" height="30">](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio))  |
+| iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata |
+| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates |
+| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/thewtex/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. |
 | ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. |
 | ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. |
 | Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. |
@@ -92,7 +92,7 @@ Want to validate a Zarr? Use one of these.
 | -------- | ------- | ------- |
 | ome-ngff-validator | [<img src="https://www.google.com/s2/favicons?sz=256&domain_url=https://ome.github.io/ome-ngff-validator/" alt="OME NGFF Validator logo" width="30" height="30">](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. |
 | ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files |
-| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O |
+| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O |
 
 ## Other tools and libraries