VT3D

VT3D visualizes three-dimensional spatially resolved transcriptomic data to enable exploration and interpretation of gene expression patterns and cell type distributions within biological samples.

Key Features:

• 2D plane projection and virtual slicing: Project gene expression onto arbitrary 2D planes and generate 2D virtual slices for examination of spatial patterns.
• Surface model plots for 3D browsing: Visualize and interactively browse 3D data using surface model plots.
• Technique compatibility: Compatible with sequencing-based methods (Stereo-seq, spatial transcriptomics, Slide-seq) and imaging-based methods (MERFISH, STARMap).
• Interactive 3D atlas database: Support creation of interactive 3D atlas databases for visualizing spatial gene expression patterns and cell niches.

Scientific Applications:

• Embryogenesis and organogenesis: Provide spatially resolved insights into gene regulatory interactions and cell type distributions during developmental processes.

Methodology:

Constructing 3D spatially resolved transcriptomic atlases from multi-view and high-dimensional data.