SpatioCell: deep integration of histology and spatial transcriptomics for profiling the cellular microenvironment at single-cell level - PubMed
3 hours ago
- #single-cell analysis
- #spatial transcriptomics
- #tumor microenvironment
- SpatioCell is a computational algorithm that integrates histology and spatial transcriptomics (ST) data to profile the cellular microenvironment at single-cell resolution.
- It uses a morpho-transcriptomic spatial reconstruction framework solved via dynamic programming to deterministically assign cell identities to precise locations, rather than inferring spot-level compositions.
- The method corrects deconvolution errors and uncovers overlooked microenvironmental features, such as the distance between cancer-associated fibroblasts (CAFs) and tumor or immune cells in triple-negative breast cancer, revealing its significance in disease progression.
- SpatioCell aims to broaden biomedical applications of ST and facilitate investigations of single-cell spatial organization, despite inherent limitations in spatial resolution of most ST datasets.