Vitessce: integrative visualization of multimodal and spatially-resolved single-cell data

Abstract

Vitessce is an open-source interactive visualization framework for exploration of multi-modal and spatially-resolved single-cell data, with a modular architecture compatible with transcriptomic, proteomic, genome-mapped, and imaging data types. Its modular, coordinated multiple view implementation facilitates a wide range of visualization tasks to support all common single-cell assays. Vitessce is a client-side web application designed to be integrated with computational analysis tools and data resources and does not require specialized server infrastructure. The software is available at http://vitessce.io.

Image-based representation of massive spatial transcriptomics datasets

“…Spacemake 37 is used for processing and basic visualization only; Vitessce 10 and Loupe browser 11 are designed for visualization purposes only; Seurat 12 and squidpy 13 offer both analyzing and viewing, but 3D visualization and sections alignment are unavailable; ST Viewer 14 is tailored to datasets generated with Spatial Transcriptomics 3 ; histoCAT 15 and Giotto Viewer 16 do not offer sections alignment. STUtility 17 offers a basic alignment, but requires manual registration for high-quality results.…”

“…A growing number of methods are developed specifically to visualize and analyze spatial transcriptomics data 3,[10][11][12][13][14][15][16][17] (Supplementary Methods). Here, we show that powerful methods from the computer vision field that have been developed by a large scientific community for decades, can alternatively be adapted to meet the challenges that spatial transcriptomics methods face.…”

Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web

“…Vitessce is a web-based framework for the interactive exploration of single-cell datasets 42 . Its flexible design allows users to author interactive visualizations which integrate epigenomics, transcriptomics, and bioimaging modalities.…”

Single-cell Spatial Explorer: Easy exploration of spatial and multimodal transcriptomics

“…Vitessce 7 (Visual integration tool for exploration of spatial single cell experiments) is an open-source interactive visualization framework for exploration of multi-modal and spatially-resolved single-cell data; It presents a modular architecture compatible with transcriptomic, proteomic, genome-mapped, and imaging data types. Vitessce can be used as a standalone web application or in Python or R environments.…”