Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

Abstract

High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can be a challenge. Here, we introduce Loopy Browser, a performant and interactive image visualization tool that runs completely in the web browser. Loopy Browser is specifically designed for fast image visualization and annotation and enables users to browse through large images and their selected features within seconds of receiving a link. We demonstrate the broad utility of Loopy Browser with images generated with two platforms: Vizgen MERFISH and 10x Genomics Visium Spatial Gene Expression. Loopy Browser along with example datasets is available at https://loopybrowser.com.

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

“…We added a third spatialLIBD app for the position differential expression results and a fourth for the Visium-SPG data. Second, both our Visium H&E (n=30 tissue sections) and Visium-SPG (n=4 tissue sections) data is available through a newly created performant web-based interactive visualization tool, called Samui Browser (30) , which allows rapid loading, visualization, and custom annotation of high resolution images and corresponding gene expression. Finally, snRNA-seq data at both fine and laminar resolution as well as pseudo-bulked Visium data ( k =9, 16, and 28) are available through iSEE apps (31) that allows users to visualize expression levels for genes of interest through violin and heatmap plots.…”

Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex

“…All source code is publicly available through GitHub and permanently archived through Zenodo at https://github.com/LieberInstitute/Visium_SPG_AD (169). Interactive websites are powered by spatialLIBD (40), iSEE (170), and samui (171). S1.…”

escheR: Unified multi-dimensional visualizations with Gestalt principles

“…This creates cognitive gaps on how to associate the disparate information or how to interpret the biological findings of this multi-dimensional information regarding their (micro-)environment or colocalization. While interactive visualizations [13][14][15] have the potential to mitigate this challenge, they are infeasible for scientific communications in static media, such as printed work. Developing a static and unified visualization that enables the simultaneous display of multiple dimensions of information is crucial for biomedical research.…”