Sopa

Sopa streamlines segmentation, aggregation, annotation, and geometric/spatial analysis of image-based spatial omics data across diverse technologies including Xenium, MERSCOPE, CosMX, MACSima, and PhenoCycler.

Key Features:

• Technology Invariance: Sopa operates uniformly across multiple spatial omics technologies including Xenium, MERSCOPE, CosMX in spatial-transcriptomics, and MACSima and PhenoCycler in multiplex imaging.
• Memory Efficiency: Sopa is optimized for memory-efficient processing of complex spatial omics datasets.
• Unified Visualizer: Sopa provides a unified visualizer for all image-based spatial omics data.
• SpatialData Framework Integration: Sopa is built upon the universal SpatialData framework.
• Comprehensive Outputs: Sopa generates web reports, visualizer files, and comprehensive data files for in-depth analysis.

Scientific Applications:

• Tissue Architecture Analysis: Sopa enables comprehensive analysis of tissue architectures and cellular organization.
• Cellular Interaction Studies: Sopa facilitates understanding of cellular interactions and tissue organization in biological systems.
• Single-Cell Resolution Analysis: Sopa supports analysis of cellular organizations and dynamics at single-cell resolution from imaging-based spatial omics.

Methodology:

Sopa is built upon the SpatialData framework and performs segmentation, transcript/channel aggregation, annotation, and geometric/spatial analysis.