From 1331b498516f565e9c628b1e058593f43e17043c Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Thu, 2 Jul 2026 09:39:53 -0400 Subject: [PATCH 1/5] Update index.md --- resources/tools/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index 7537acd0..47098fa3 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -120,3 +120,5 @@ Libraries that support the rendering and navigation of OME-Zarr data, but that a | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | | idetik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/chanzuckerberg/idetik) | A library for building web-based image viewers. | +| Viv | [Viv logo](https://github.com/hms-dbmi/viv) | A JavaScript library that provides DeckGL-compatible layers for rendering OME-Zarr images on the web. | +| Pluot | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/keller-mark/pluot) | Rust and WebGPU-based rendering of OME-Zarr images with bindings to JavaScript/React, Python, and R. | From e5c7218de5fe8ead44c00f71ae39a81a4172ca0b Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Thu, 2 Jul 2026 09:48:31 -0400 Subject: [PATCH 2/5] Update index.md --- resources/tools/index.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 47098fa3..3fcd3597 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -44,7 +44,9 @@ Want to view a Zarr? Use one of these. | Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A 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 | +| Vitessce | [Viv logo](https://github.com/vitessce/vitessce) | A framework for interactive visualization of single-cell and spatial multi-omics data, including support for multi-scale, multiplexed OME-Zarr images. Vitessce is built using the [Viv](github.com/hms-dbmi/viv) library. | +| Vizarr | [Viv logo](github.com/hms-dbmi/vizarr) | A minimal client-side application for viewing multi-scale, multiplexed OME-Zarr images (including HCS images) online and in notebooks. Vizarr is built using the [Viv](github.com/hms-dbmi/viv) library. | +| Avivator | [Viv logo]([https://github.com/hms-dbmi/viv](https://github.com/hms-dbmi/viv/tree/main/sites/avivator)) | A lightweight demo website that showcases the [Viv](github.com/hms-dbmi/viv) library for rendering multi-scale, multiplexed OME-Zarr images. | | Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | | WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | From 5b9449ebc25226e5e622bad7163ef3a7e9d7973c Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Thu, 2 Jul 2026 09:52:56 -0400 Subject: [PATCH 3/5] Update index.md --- resources/tools/index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 3fcd3597..d0eff91f 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -44,9 +44,9 @@ Want to view a Zarr? Use one of these. | Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Vitessce | [Viv logo](https://github.com/vitessce/vitessce) | A framework for interactive visualization of single-cell and spatial multi-omics data, including support for multi-scale, multiplexed OME-Zarr images. Vitessce is built using the [Viv](github.com/hms-dbmi/viv) library. | -| Vizarr | [Viv logo](github.com/hms-dbmi/vizarr) | A minimal client-side application for viewing multi-scale, multiplexed OME-Zarr images (including HCS images) online and in notebooks. Vizarr is built using the [Viv](github.com/hms-dbmi/viv) library. | -| Avivator | [Viv logo]([https://github.com/hms-dbmi/viv](https://github.com/hms-dbmi/viv/tree/main/sites/avivator)) | A lightweight demo website that showcases the [Viv](github.com/hms-dbmi/viv) library for rendering multi-scale, multiplexed OME-Zarr images. | +| Vitessce | [Viv logo](https://github.com/vitessce/vitessce) | A framework for interactive visualization of single-cell and spatial multi-omics data, including support for multi-scale, multiplexed OME-Zarr images. Vitessce is built using the [Viv](https://github.com/hms-dbmi/viv) library. | +| Vizarr | [Viv logo](https://github.com/hms-dbmi/vizarr) | A minimal client-side application for viewing multi-scale, multiplexed OME-Zarr images (including HCS images) online and in notebooks. Vizarr is built using the [Viv](https://github.com/hms-dbmi/viv) library. | +| Avivator | [Viv logo]([https://github.com/hms-dbmi/viv](https://github.com/hms-dbmi/viv/tree/main/sites/avivator)) | A lightweight demo website that showcases the [Viv](https://github.com/hms-dbmi/viv) library for rendering multi-scale, multiplexed OME-Zarr images. | | Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | | WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | From adc06425059036e4ea212f1f82838b7f5f354616 Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Thu, 2 Jul 2026 09:54:05 -0400 Subject: [PATCH 4/5] Update index.md --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index d0eff91f..46508c86 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -46,7 +46,7 @@ Want to view a Zarr? Use one of these. | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Vitessce | [Viv logo](https://github.com/vitessce/vitessce) | A framework for interactive visualization of single-cell and spatial multi-omics data, including support for multi-scale, multiplexed OME-Zarr images. Vitessce is built using the [Viv](https://github.com/hms-dbmi/viv) library. | | Vizarr | [Viv logo](https://github.com/hms-dbmi/vizarr) | A minimal client-side application for viewing multi-scale, multiplexed OME-Zarr images (including HCS images) online and in notebooks. Vizarr is built using the [Viv](https://github.com/hms-dbmi/viv) library. | -| Avivator | [Viv logo]([https://github.com/hms-dbmi/viv](https://github.com/hms-dbmi/viv/tree/main/sites/avivator)) | A lightweight demo website that showcases the [Viv](https://github.com/hms-dbmi/viv) library for rendering multi-scale, multiplexed OME-Zarr images. | +| Avivator | [Viv logo](https://github.com/hms-dbmi/viv/tree/main/sites/avivator) | A lightweight demo website that showcases the [Viv](https://github.com/hms-dbmi/viv) library for rendering multi-scale, multiplexed OME-Zarr images. | | Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | | WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | From 86461251d1e1c2fe146822e1f160ad94d1110694 Mon Sep 17 00:00:00 2001 From: Mark Keller <7525285+keller-mark@users.noreply.github.com> Date: Fri, 3 Jul 2026 16:25:52 -0400 Subject: [PATCH 5/5] Update index.md --- resources/tools/index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 46508c86..82e84b32 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -44,9 +44,9 @@ Want to view a Zarr? Use one of these. | Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Vitessce | [Viv logo](https://github.com/vitessce/vitessce) | A framework for interactive visualization of single-cell and spatial multi-omics data, including support for multi-scale, multiplexed OME-Zarr images. Vitessce is built using the [Viv](https://github.com/hms-dbmi/viv) library. | -| Vizarr | [Viv logo](https://github.com/hms-dbmi/vizarr) | A minimal client-side application for viewing multi-scale, multiplexed OME-Zarr images (including HCS images) online and in notebooks. Vizarr is built using the [Viv](https://github.com/hms-dbmi/viv) library. | -| Avivator | [Viv logo](https://github.com/hms-dbmi/viv/tree/main/sites/avivator) | A lightweight demo website that showcases the [Viv](https://github.com/hms-dbmi/viv) library for rendering multi-scale, multiplexed OME-Zarr images. | +| Vitessce | [Viv logo](https://github.com/vitessce/vitessce) | Framework for visualization of spatial single-cell data, built using [Viv](https://github.com/hms-dbmi/viv). | +| Vizarr | [Viv logo](https://github.com/hms-dbmi/vizarr) | Web app for viewing multi-scale, multiplexed OME-Zarr images (incl. HCS), built using [Viv](https://github.com/hms-dbmi/viv). | +| Avivator | [Viv logo](https://avivator.gehlenborglab.org/) | Demo website that showcases the [Viv](https://github.com/hms-dbmi/viv) rendering library. | | Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | | WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets |