From b1e7c383fb1cdb60a15cc2c4a32f755df150b8e4 Mon Sep 17 00:00:00 2001 From: Jonas Windhager Date: Fri, 17 Nov 2023 14:58:46 +0100 Subject: [PATCH] add tools/libraries + descriptions & evaluations --- tools/index.md | 112 ++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 88 insertions(+), 24 deletions(-) diff --git a/tools/index.md b/tools/index.md index 41c280a2..b3b0d5d0 100644 --- a/tools/index.md +++ b/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 . + + +## 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).