Merge pull request #220 from jwindhager/tools

add tools/libraries + descriptions & evaluations

tools/index.md

@@ -1,94 +1,158 @@
 # Tools
 
-A list of tools which support OME-Zarr. These are developed by various members of the NGFF community.
+A list of tools and libraries with OME-Zarr support. These are developed by various members of the OME-NGFF community. If you think your tool/library should be listed here, please [open a pull request](https://github.com/ome/ngff).
 
-## Visualization Tools
+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
-The [napari viewer](https://github.com/napari/napari) supports OME-Zarr with the [napari-ome-zarr plugin](https://github.com/ome/napari-ome-zarr)
+<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
+
+### Viv (Avivator, Vizarr, Vitessce, ...)
 <https://github.com/hms-dbmi/viv>
 
-<iframe style="width: 100%; height: 500px" name="vizarr" src="https://hms-dbmi.github.io/vizarr/v0.1/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4495402.zarr">
-</iframe>
+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
+
+### WEBKNOSSOS
 <https://github.com/scalableminds/webknossos>
 
+An open-source tool for annotating and exploring large 3D image datasets.
+
 
-### website-3d-cell-viewer
+### 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).
 
-## Utilities
+
+## Tools for converting image files to OME-Zarr
 
 ### bioformats2raw
 <https://github.com/glencoesoftware/bioformats2raw>
 
-
-### ome-ngff-validator
-<https://github.com/ome/ome-ngff-validator>
+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.
+
+
+## Libraries for reading/writing OME-Zarr files
+
+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/.
 
-## Libraries
 
-### aicsimageio
+### AICSImageIO
 <https://github.com/AllenCellModeling/aicsimageio>
 
+Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python.
 
-### tensorstore
-<https://github.com/google/tensorstore/>
 
+### bfio
+<https://github.com/PolusAI/bfio>
 
-### Fractal
-<https://github.com/fractal-analytics-platform/fractal>
+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.
+
+
+### 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.
 
-### bfio
-<https://github.com/PolusAI/bfio>
 
+### ITKIOOMEZarrNGFF
+<https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF>
 
-### SpatialData
-<https://github.com/scverse/spatialdata>
+An ITK external module for IO of images stored in Zarr-backed OME-NGFF file format.
+
+
+## Other tools and libraries
+
+### Fractal
+<https://github.com/fractal-analytics-platform/fractal>
+
+A framework to process high content screening data at scale and to prepare it for interactive visualization.
 
 
 ### Nyxus
 <https://github.com/PolusAI/nyxus>
 
+A scalable library for calculating features from intensity-label image data.
 
-### ITKIOOMEZarrNGFF
-<https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF>
+
+### 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).