ScopeViewer：一种基于浏览器的空间转录组学数据可视化解决方案。

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

作者信息

Luo Danni, Robertson Sophie, Zhan Yuanchun, Rong Ruichen, Wang Shidan, Jiang Xi, Yang Sen, Palmer Suzette, Jia Liwei, Li Qiwei, Xiao Guanghua, Zhan Xiaowei

机构信息

Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center.

Paul Allen School of Computer Science & Engineering, University of Washington.

出版信息

bioRxiv. 2023 Jul 25:2023.07.24.549256. doi: 10.1101/2023.07.24.549256.

DOI:10.1101/2023.07.24.549256

PMID:37546786

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10401999/

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: https://datacommons.swmed.edu/scopeviewer.

摘要

动机

空间转录组学（ST）能够在特定空间背景和组织形态内对分子特征进行高分辨率的探究。尽管具有潜力，但由于处理、共享和可视化大型图像数据集以及分子信息的复杂性，ST数据的可视化是一项具有挑战性的任务。

结果

我们推出了ScopeViewer，这是一款基于浏览器的软件，旨在克服这些挑战。ScopeViewer提供以下功能：（1）它能在各种缩放级别可视化大型图像数据及相关注释，便于对数据进行细致探索；（2）它能对原始图像及其注释进行双重交互式查看，全面理解上下文；（3）它以优化带宽显示空间分子特征，确保用户体验流畅；（4）它通过避免数据传输来增强数据安全性。