ISH Analysis and RNA Quantification

In situ hybridisation (ISH,CISH, FISH, DISH) using methods such as RNAscope®, is a popular approach for the evaluation of changes in biomarker expression or a particular drug response effect in tissues, especially in the case of novel biomarkers where robust, well validated antibodies are not commercially available.

RISH Whole Image

Analysis Approach

A custom algorithm is developed that accurately identifies and segments the whole tissue section into regions of interest (ROI). Specific ROI can then be chosen to perform highly detailed quantification of ISH signal within individual cells across a chosen tissue. Once the algorithm is completed, it is applied to all tissue section images in the study in a consistent, automated and objective manner to generate highly detailed information, enabling robust statistical analysis and in-depth interpretation.

RISH Example

  • Mean number of RNA spots per cell across a whole tissue or within a specified tissue ROI.
  • Classification (4 classes) of individual cells based on number of spots.
  • Classification of cells based on RNA localised in whole cell or within a specific sub cellular compartment.
  • Identification and quantification of cells with co-localised ISH probes.
  • Quantification of chromogenic or fluorescent labelled probes.

RISH example data


  • Receive highly detailed data quantifying RNA expression on a cell by cell basis across a whole tissue section or within defined regions of interest.
  • Our automated batch analysis service objectively analyses each section using the same algorithm to reduce variability and improve data quality and interpretation.