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Modular pipeline architecture organized by functional category (A) ROI image data input and signal enhancement modules for importing and enhancing RNAscope ROI images; (B) Object identification modules for qualitative and quantitative assessments of nuclear, cytoplasmic, and extracellular localizations with their respective markers; (C) Filtering and classification modules for cell typing and intermarker association quantification; (D) Neighborhood analysis modules for evaluating intermarker associations and marker density; (E) Measurement and visualization modules for spatial and tissue profile assessment. Static modules (gray) required minimal adjustment across tissue types. Variable modules (blue) are slide- and/or tissue-specific, requiring additional customization for specific gene or intermarker associations.

Journal: STAR Protocols

Article Title: Protocol for spatial analysis of multiple markers across adjacent tissue sections captured by RNAscope using CellProfiler

doi: 10.1016/j.xpro.2025.103914

Figure Lengend Snippet: Modular pipeline architecture organized by functional category (A) ROI image data input and signal enhancement modules for importing and enhancing RNAscope ROI images; (B) Object identification modules for qualitative and quantitative assessments of nuclear, cytoplasmic, and extracellular localizations with their respective markers; (C) Filtering and classification modules for cell typing and intermarker association quantification; (D) Neighborhood analysis modules for evaluating intermarker associations and marker density; (E) Measurement and visualization modules for spatial and tissue profile assessment. Static modules (gray) required minimal adjustment across tissue types. Variable modules (blue) are slide- and/or tissue-specific, requiring additional customization for specific gene or intermarker associations.

Article Snippet: Scan and visualize RNAscope slides using a pathology imaging system (e.g., Vectra Polaris Automated Quantitative Pathology Imaging System [Akoya Biosciences, Perkin Elmer]), as discussed by Sari et al . 4.

Techniques: Functional Assay, RNAscope, Marker