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bioRxiv · 10.1101/2023.07.24.549256

ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data

Luo, D.·Robertson, S.·Zhan, Y.·Rong, R.·Wang, S.·Jiang, X.·Yang, S.·Palmer, S.·Jia, L.·Li, Q.·Xiao, G.·Zhan, X.
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Abstract

MotivationSpatial 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. ResultsWe 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. AvailabilityScopeViewer is available at: https://datacommons.swmed.edu/scopeviewer ContactXiaowei.Zhan@UTSouthwestern.edu, Guanghua.Xiao@UTSouthwestern.edu Supplementary informationSupplementary data are available at Bioinformatics online.

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Luo, D., Robertson, S., Zhan, Y., Rong, R., Wang, S., Jiang, X., Yang, S., Palmer, S., Jia, L., Li, Q., Xiao, G., Zhan, X.. 2023-07-25. ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data. https://doi.org/10.1101/2023.07.24.549256

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