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@@ -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 .
+
+
+## Image viewers with OME-Zarr support
### AGAVE
+A desktop application for viewing multichannel volume data.
+
### ITKWidgets
+A Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
+
### MoBIE/BDV
+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)
+
+
+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
+A WebGL-based viewer for volumetric data.
-### Viv
+
+### Viv (Avivator, Vizarr, Vitessce, ...)
-
+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
+
+### WEBKNOSSOS
+An open-source tool for annotating and exploring large 3D image datasets.
+
-### website-3d-cell-viewer
+### AICS Image Viewer
+A browser-based volume viewer built with React and WebGL (Three.js).
-## Utilities
+
+## Tools for converting image files to OME-Zarr
### bioformats2raw
-
-### 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
+A GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF.
+
+
### 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
+Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python.
-### tensorstore
-
+### bfio
+
-### Fractal
-
+A Python interface to Bioformats using jpype for direct access to the library.
### Bio-Formats
+A standalone Java library for reading and writing life sciences image file formats.
+
+
+### ngff-zarr
+
+
+A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
+
+
+### multiscale-spatial-image
+
+
+Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
+
### ome-zarr-py
+A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME NGFF spec.
-### bfio
-
+### ITKIOOMEZarrNGFF
+
-### SpatialData
-
+An ITK external module for IO of images stored in Zarr-backed OME-NGFF file format.
+
+
+## Other tools and libraries
+
+### Fractal
+
+
+A framework to process high content screening data at scale and to prepare it for interactive visualization.
### Nyxus
+A scalable library for calculating features from intensity-label image data.
-### ITKIOOMEZarrNGFF
-
+
+### ome-ngff-validator
+
+
+Web page for validating OME-NGFF files.
+
+
+### SpatialData
+
+
+An open and universal framework for processing spatial omics data.
+
+
+### tensorstore
+
+
+Library for reading and writing large multi-dimensional arrays (e.g., Zarr).