Image analysis with ISH (FISH, CISH and RNA Scope slides)

Quantification of in situ hybridization slides

For CISH/FISH slides, the algorithm allows to detect and quantify the gene and its control, and to segment the nuclei if necessary. The result thus proposes a number of genes and total control on a region of interest, or a classification of the nuclei based on the amplification of the gene.

For RNA Scope slides, the algorithm allows to detect and quantify the gene of interest, and to segment the nuclei if needed. The result can be a total gene number over a region of interest, or a nucleus classification based on the gene copy number.

image analysis with ISH digital pathology

The protocol

The stages of image analysis with ISH algorithm are as follows:

  • Nuclei segmentation
    A nuclei segmentation is performed on luminance on one of the color plans to eliminate the rest of the tissue. A separation algorithm is then applied to individualize the nuclei.
  • Genes segmentation
    Each gene is segmented on its own color channel. A dot and / or surface approach is available.
  • Classification
    For each nucleus, a number of copies of the gene is estimated, eventually including its control markers. Each nucleus is then sorted according to the number of copies or to the amplification ratio. 

The results present the number of valid segmented nuclei as well as a class according to the number of copies or to the amplification ratio. A color representation and a gallery mode allow fast validation.