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Improved Tools Docs #273

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Expand Up @@ -4,163 +4,45 @@ A list of tools and libraries with OME-Zarr support. These are developed by vari

In addition to this collection, an evaluation of selected tools/libraries is available on <https://ome.github.io/ome-ngff-tools/>.


## Image viewers with OME-Zarr support

### AGAVE
<https://github.com/allen-cell-animated/agave>

A desktop application for viewing multichannel volume data.


### ITKWidgets
<https://github.com/InsightSoftwareConsortium/itkwidgets>

A Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.


### MoBIE/BDV
<https://github.com/mobie/mobie-viewer-fiji>

A Fiji plugin for exploring and sharing big multi-modal image and associated tabular data.


### napari
<https://github.com/napari/napari>

A fast, interactive, multi-dimensional image viewer for Python that supports OME-Zarr with the [napari-ome-zarr](https://github.com/ome/napari-ome-zarr) plugin.


### Neuroglancer
<https://github.com/google/neuroglancer>

A WebGL-based viewer for volumetric data.


### Viv (Avivator, Vizarr, Vitessce, ...)
<https://github.com/hms-dbmi/viv>

A WebGL-powered 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.

<iframe style="width: 100%; height: 500px" name="vizarr" src="https://hms-dbmi.github.io/vizarr/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4495402.zarr"></iframe>


### WEBKNOSSOS
<https://github.com/scalableminds/webknossos>

An open-source tool for annotating and exploring large 3D image datasets.


### AICS Image Viewer
<https://github.com/allen-cell-animated/website-3d-cell-viewer>

A browser-based volume viewer built with React and WebGL (Three.js).


## Tools for converting image files to OME-Zarr

### bioformats2raw
<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.


### NGFF-Converter
<https://github.com/glencoesoftware/NGFF-Converter>

A GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF.


### stack_to_multiscale_ngff
<https://github.com/CBI-PITT/stack_to_multiscale_ngff>

A tool for converting multi-terabyte stacks of images into a multiscale OME-NGFF Zarr.


### BatchConvert
<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.


## Libraries for reading/writing OME-Zarr files
## Image Viewers
| Name | Link | Description |
| -------- | ------- | ------- |
| AGAVE | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/allen-cell-animated/agave) | A desktop application for viewing multichannel volume data. |
| ITKWidgets | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/itkwidgets) | A Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry. |
| MoBIE/BDV | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mobie/mobie-viewer-fiji) | A Fiji plugin for exploring and sharing big multi-modal image and associated tabular data. |
| napari | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/napari/napari) | A fast, interactive, multi-dimensional image viewer for Python that supports OME-Zarr with the [napari-ome-zarr](https://github.com/ome/napari-ome-zarr) plugin. |
| Neuroglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/google/neuroglancer) | A WebGL-based viewer for volumetric data. |
| Viv (Avivator, Vizarr, Vitessce, ...) | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/hms-dbmi/viv) | A WebGL-powered 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. |
| WEBKNOSSOS | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scalableminds/webknossos) | An open-source tool for annotating and exploring large 3D image datasets. |
| 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
| 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. |
| NGFF-Converter | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/NGFF-Converter) | A GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF. |
| 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-NGFF Zarr. |
| 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. |

## File Reading/Writing

Various libraries for reading/writing OME-Zarr files in Python were evaluated as part of the BioVisionCenter "Next generation bioimage analysis workflows hackathon" 2023 in Zurich, Switzerland: https://github.com/jwindhager/ome-ngff-readers-writers/.


### bfio
<https://github.com/PolusAI/bfio>

A Python interface to Bioformats using jpype for direct access to the library.


### Bio-Formats
<https://github.com/ome/bioformats>

A standalone Java library for reading and writing life sciences image file formats.


### BioIO
<https://github.com/bioio-devs/bioio>

(formerly AICSImageIO <https://github.com/AllenCellModeling/aicsimageio>)

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python.


### ngff-zarr
<https://github.com/thewtex/ngff-zarr>

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.


### multiscale-spatial-image
<https://github.com/spatial-image/multiscale-spatial-image>

Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.


### ome-zarr-py
<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 NGFF spec.


### ITKIOOMEZarrNGFF
<https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF>

An ITK external module for IO of images stored in Zarr-backed OME-NGFF file format.


## Other tools and libraries

### Fractal
<https://fractal-analytics-platform.github.io/>

A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization.


### Nyxus
<https://github.com/PolusAI/nyxus>

A scalable library for calculating features from intensity-label image data.


### ome-ngff-validator
<https://github.com/ome/ome-ngff-validator>

Web page for validating OME-NGFF files.


### SpatialData
<https://github.com/scverse/spatialdata>

An open and universal framework for processing spatial omics data.


### tensorstore
<https://github.com/google/tensorstore/>

Library for reading and writing large multi-dimensional arrays (e.g., Zarr).
| 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. |
| BioIO | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/bioio-devs/bioio) | (formerly AICSImageIO <https://github.com/AllenCellModeling/aicsimageio>) Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python. |
| 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. |
| 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-NGFF. |
| 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 NGFF spec. |
| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in Zarr-backed OME-NGFF file format. |

## Other Tools and Libraries
| Name | Link | Description |
| -------- | ------- | ------- |
| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. |
| 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). |
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