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VT3D: a visualization toolbox for 3D transcriptomic data.

Lidong Guo1, Yao Li2, Yanwei Qi2

  • 1College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China.

Journal of Genetics and Genomics = Yi Chuan Xue Bao
|April 13, 2023
PubMed
Summary
This summary is machine-generated.

VT3D is a new visualization toolbox for exploring three-dimension (3D) spatially resolved transcriptomic data. This tool enhances understanding of gene expression and cell distribution, accelerating biological discovery.

Keywords:
3D visualizationData sharingMERFISHSpatial transcriptomicsSpatially resolved transcriptomicsStereo-seqVirtual slice

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Visualization

Background:

  • Three-dimension (3D) spatially resolved transcriptomic atlases are crucial for understanding gene expression and cell distribution.
  • Existing visualization tools are limited, hindering the full application of 3D transcriptomic data.
  • Advancements in high-throughput techniques generate complex, multi-view datasets.

Purpose of the Study:

  • To introduce VT3D, an accessible visualization toolbox for exploring 3D transcriptomic data.
  • To enable interactive analysis of gene expression patterns and cell type distribution in biological samples.
  • To bridge the gap between researchers and the application of spatially resolved transcriptomics.

Main Methods:

  • VT3D allows projection of gene expression onto any 2D plane and creation of virtual 2D slices.
  • It provides interactive 3D data browsing with surface model plots.
  • The toolbox supports both standalone and web-based server modes, compatible with various sequencing and imaging techniques.

Main Results:

  • VT3D was successfully applied to multiple datasets from popular techniques like Stereo-seq, spatial transcriptomics, Slide-seq, MERFISH, and STARMap.
  • A 3D atlas database was constructed, enabling interactive data browsing.
  • The tool facilitates exploration of complex spatial gene expression patterns.

Conclusions:

  • VT3D effectively visualizes and enables interactive exploration of 3D spatially resolved transcriptomic data.
  • The toolbox accelerates research in developmental biology, such as embryogenesis and organogenesis.
  • VT3D enhances the accessibility and impact of advanced transcriptomic analysis.