ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data
Abstract
Motivation
Spatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing and visualizing large image datasets together with molecular information.
Results
We introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) It visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) It enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) It displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) It bolsters data security by circumventing data transfers.
Availability
ScopeViewer is available at: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://datacommons.swmed.edu/scopeviewer">https://datacommons.swmed.edu/scopeviewer</ext-link>
Contact
<email>Xiaowei.Zhan@UTSouthwestern.edu</email> , <email>Guanghua.Xiao@UTSouthwestern.edu</email>
Supplementary information
Supplementary data are available at Bioinformatics online.
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