TissUUmaps

TissUUmaps visualizes high-resolution whole-slide images together with spatially resolved molecular data to enable exploration and analysis of spatial gene expression and tissue morphology.

Key Features:

• Multi-resolution visualization: Provides multi-resolution visualization of spatially resolved gene expression and tissue morphology for exploration at different scales.
• Efficient data handling with image pyramids: Employs image pyramids for efficient storage, distribution, and visualization of large whole-slide images and associated marker datasets, enabling handling of millions of data points.
• Overlay of molecular and per-cell data: Overlays spatial markers, including gene expression and per-cell data, onto whole-slide images and supports definition of regions of interest.
• Region-of-interest extraction and local statistics: Extracts regions of interest and computes local statistics from spatial marker data.

Scientific Applications:

• Oncology: Visualizing spatial gene expression and tissue morphology to analyze tumor microenvironment and spatial heterogeneity.
• Pathology: Correlating histological features on whole-slide images with molecular marker distributions for research and diagnostic investigations.
• Developmental biology: Studying spatial patterns of gene expression and tissue organization during development.
• Translational research: Integrating imaging and molecular datasets to support translational studies linking basic discoveries to clinical applications.

Methodology:

Integrates high-resolution whole-slide imaging with molecular marker data and leverages image pyramids for multi-resolution visualization and efficient data management.