Fig. 1: Overview of QuantISH image analysis pipeline. | Laboratory Investigation

Fig. 1: Overview of QuantISH image analysis pipeline.

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

Fig. 1

A Cropping chromogenic tissue microarray (TMA) spots. B Separating the brown chromogenic signals from the original TMA images using the color separation and background noise suppression steps. C Cleaning the original chromogenic image from the separated marker channel (brown) to preserve the cellular morphology under a high level of marker expression for further segmentation in the nuclear staining (blue). D Cell segmentation of a cleaned nuclear staining channel for a TMA image. Different colors represent different objects (cells). E Cell type classification and segment expansion of the nuclear segments to cover the cell cytoplasm. F Using the separated marker channel to quantify RNA signals inside each TMA spot and each specific cell type. G Downstream analysis of average expression and expression variability per sample/patient and their association to patients’ survival.

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