StImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration.

ABSTRACT: Spatial transcriptomics (ST) integrates gene expression data with the spatial organization of cells and their associated histology, offering unprecedented insights into tissue biology. While existing methods incorporate either location-based or histology-informed information, none fully synergize gene expression, histological features, and precise spatial coordinates within a unified framework. Moreover, these methods often exhibit inconsistent performance across diverse datasets and conditions. Here, we introduce stImage, an open-source R package that provides a comprehensive and flexible solution for ST analysis. By generating deep learning-derived histology features and offering 54 integrative strategies, stImage seamlessly combines transcriptional profiles, histology images, and spatia

SUBMITTER: Wang Y 

PROVIDER: S-EPMC12409783 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature