MCMICRO

MCMICRO processes highly multiplexed, multi-channel whole slide tissue images to generate single-cell feature data while preserving spatial context for molecular and spatial analysis.

Key Features:

• End-to-end processing: Executes stitching and registration, segmentation, and single-cell feature extraction for multiplexed tissue imaging data.
• Stitching and registration: Performs image stitching and spatial registration of multi-channel whole slide images.
• Segmentation: Performs segmentation to delineate single-cell regions from multiplexed images.
• Single-cell feature extraction: Extracts per-cell measurements from segmented regions to produce single-cell data.
• Containerized modular workflow: Implements modular, containerized components to enable portable deployment across diverse computing environments and support reproducibility.
• Multi-platform compatibility: Demonstrated on images from various tissues and tumors acquired with multiple imaging platforms and accepts large, multi-channel whole slide image inputs.
• Preservation of spatial context: Maintains spatial relationships between cells when transforming images into single-cell data.

Scientific Applications:

• Single-cell spatial molecular analysis: Enables molecular analysis of single cells within preserved spatial context from highly multiplexed tissue images.
• Tumor and tissue imaging studies: Applied to the analysis of tissues and tumors across multiple imaging platforms.
• Systems pharmacology: Supports systems pharmacology research that requires spatially resolved single-cell data.
• Advancing tissue imaging software development: Provides a foundation for development and benchmarking of tissue imaging analysis methods.

Methodology:

Processing steps explicitly include stitching and registration, segmentation, and single-cell feature extraction; components are modular and containerized for deployment.