iVistoSeg

iVistoSeg processes high-resolution histological and immunofluorescent images from the 10× Genomics Visium platform using a MATLAB-based pipeline and integrates image-derived metrics with spatially resolved transcriptomics to link tissue morphology and gene expression.

Key Features:

• Integration of imaging and transcriptomic data: Processes high-resolution histological or immunofluorescent images that accompany Visium (10× Genomics) RNA sequencing data to correlate morphology with gene expression.
• Image processing and analysis: Implements MATLAB-based image-processing utilities to extract image-derived metrics from high-resolution images.
• Interactive visualization: Provides interactive visualization capabilities for joint exploration of imaging and spatial gene expression datasets.
• Seamless data integration: Exports outputs compatible with downstream analyses in R and Python to enable integration with spatial gene expression workflows.

Scientific Applications:

• Developmental biology: Enables analysis of spatial heterogeneity and the relationship between morphology and gene expression during development.
• Cancer research: Facilitates investigation of spatial gene expression patterns and tissue organization relevant to cancer studies.
• Neuroscience: Supports mapping of spatial gene expression in neural tissues to relate anatomical features to molecular profiles.

Methodology:

MATLAB-based pipeline that processes high-resolution histological and immunofluorescent images accompanying 10× Genomics Visium RNA sequencing data, extracts image-derived metrics, provides interactive visualization, and exports outputs compatible with R and Python.