From fffe3f254b1b89777796df599a0838d29a361ee9 Mon Sep 17 00:00:00 2001 From: huxfo013 Date: Wed, 20 Nov 2024 10:29:22 -0600 Subject: [PATCH] Move list of tools into markdown tables --- tools/index.md | 196 ++++++++++--------------------------------------- 1 file changed, 39 insertions(+), 157 deletions(-) diff --git a/tools/index.md b/tools/index.md index 1a4a62ec..efe1eec6 100644 --- a/tools/index.md +++ b/tools/index.md @@ -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 . - -## 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 - - -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 (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 - - -An open-source tool for annotating and exploring large 3D image datasets. - - -### AICS Image Viewer - - -A browser-based volume viewer built with React and WebGL (Three.js). - - -## Tools for converting image files to OME-Zarr - -### bioformats2raw - - -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. - - -### 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 - - -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. - - -### BioIO - - -(formerly AICSImageIO ) - -Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python. - - -### 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. - - -### ITKIOOMEZarrNGFF - - -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 OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. - - -### Nyxus - - -A scalable library for calculating features from intensity-label image data. - - -### 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). +| 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 ) 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). | \ No newline at end of file