SSAM-lite

SSAM-lite performs segmentation-free cell-typing of single-molecule spatially resolved transcriptomics (SRT) data by aggregating mRNA molecule coordinates into cell-specific expression profiles for spatially informed transcriptomic analysis.

Key Features:

• Segmentation-free analysis: Aggregates single-molecule mRNA coordinates into cellular expression profiles without requiring nucleus- or membrane-based boundary identification.
• Single-molecule SRT compatibility: Designed to operate on single-molecule spatially resolved transcriptomics datasets and single-molecule SRT methods.
• Computational efficiency: Optimized for rapid processing of complex tissue samples to reduce computation time.
• Parameter optimization on subsets: Allows optimization of analysis parameters on data subsets prior to application to entire datasets.

Scientific Applications:

• Cell-typing in tissues: Produces cell-specific expression profiles to assign cell types within their spatial context.
• Neuroscience: Enables spatial characterization of gene expression in neural tissues, with example use in the mouse somatosensory cortex.
• Developmental biology and spatial functional studies: Supports investigations of spatial organization of gene expression and cellular functions at single-molecule resolution.

Methodology:

Aggregates single-molecule mRNA coordinates into cellular features using segmentation-free algorithms that do not require prior identification of cell boundaries.