QuantISH: RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability.

ABSTRACT: RNA in situ hybridization (RNA-ISH) is a powerful spatial transcriptomics technology to characterize target RNA abundance and localization in individual cells. This allows analysis of tumor heterogeneity and expression localization, which are not readily obtainable through transcriptomic data analysis. RNA-ISH experiments produce large amounts of data and there is a need for automated analysis methods. Here we present QuantISH, a comprehensive open-source RNA-ISH image analysis pipeline that quantifies marker expressions in individual carcinoma, immune, and stromal cells on chromogenic or fluorescent in situ hybridization images. QuantISH is designed to be modular and can be adapted to various image and sample types and staining protocols. We show that in chromogenic RNA in situ hybridizat

SUBMITTER: Jamalzadeh S 

PROVIDER: S-EPMC9249626 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature