STUtility

STUtility provides integration and analysis of spatial transcriptomics and associated imaging data from the 10x Genomics Visium platform to align consecutive tissue sections and construct three-dimensional maps of gene expression.

Key Features:

• Image processing and alignment: Processes tissue images and aligns stacked Visium experiments from consecutive sections to enable combined spatial analyses.
• Standardized data transformations: Applies standardized transformations and workflows compatible with the Seurat framework for consistent data normalization and handling.
• Regional annotation: Supports annotation of tissue regions for focused spatial analyses and comparison across sections.
• 3D visualization and rendering: Renders combined section data in a three-dimensional model framework to visualize spatial distribution of gene expression.
• Integration with Bioconductor: Interfaces with Bioconductor packages to leverage additional bioinformatics tools for spatially resolved RNA-seq and image data analysis.

Scientific Applications:

• Developmental biology: Enables mapping of spatial gene expression across consecutive sections to study tissue patterning and morphogenesis.
• Cancer research: Facilitates analysis of tumor microenvironment spatial organization and regional gene-expression heterogeneity.
• Tissue engineering: Supports characterization of engineered tissue architectures by providing spatially resolved molecular profiles in three dimensions.

Methodology:

Image processing, alignment of stacked Visium experiments, standardized data transformations via the Seurat framework, regional annotation, 3D rendering of combined datasets, and integration with Bioconductor packages.