18. January 2023

Understanding the Different Types of FISH Evaluations

Advanced and robust in-situ hybridization techniques are required to study the genetics of cell and molecular biology both accurately and efficiently. Fluorescence in-situ hybridization – abbreviated FISH – was developed to enable researchers to analyze the genetics of cells by detecting gene sequences directly on chromosomes within the nuclei, ultimately allowing clinicians to clinically diagnose disorders and abnormalities in patients via evaluation of this visual data [1]. This blog post represents an introduction to the advantages of FISH and the different types of FISH evaluations, as well as an overview of how the information from FISH evaluations can be applied in biomedical laboratories for research areas such as cancer.

What are the advantages of performing FISH evaluations?

FISH is a sequencing-based method that operates via fluorescent oligonucleotide probes that attach to specific complementary parts of a cell’s chromosome and signals its attachment and location via fluorescence imaging [1]. After this data is assesed, scientists can quickly and easily identify gene expression profiles or genetic abnormalities flagged by the probes and analyze what type of abnormality was detected via the FISH evaluations. Because of this capability, FISH possesses high throughput, accuracy, specificity, and is more time efficient in comparison to traditional methods of cell genomics such as karyotype analysis [1].

There are many types of different samples to which FISH can be applied, including tissue samples, cells, microbes,  telomeres, to detect DNA damage or even identify the expression of gene patterns in the brain [1]. Furthermore, various types of FISH evaluations can be conducted with advanced tissue cytometry  platforms such as TissueFAXS and StrataQuest (TissueGnostics) to extract usable data from these research experiments.

Capabilities of FISH evaluations

Other types of in-situ detection methods were developed to enhance existing FISH evaluations and can further supplement the analysis of complex biomedical research concepts such as cancer and tumor biology. For example, chromogenic in-situ hybridization (CISH) uses enzymatic reactions instead of fluorescence dye (like in FISH) to detect the targets [2]. Another similar method is RNAScope, which is capable of detecting RNA instead of DNA sequences. Precisely in the tumor microenvironment, RNAscope staining can spatially map cells, characterize genetic signatures, classify heterogeneous cell types and circulating tumor cells, and analyze cellular response to cancer drugs [2]. All these processes rely on robust imaging platforms to analyze and quantify the extracted visual data into translatable information for clinical decisions based on FISH evaluations.

TissueGnostics as a leader in developing solutions for FISH evaluations

TissueGnostics is a leading life sciences company that provides cutting-edge tissue cytometers as solutions for the acquisition and analysis of different FISH experiments. Experienced in bringing together scientific workflows with innovative imaging and analysis techniques, TissueGnostics allows users to analyse FISH experiments. TissueGnostics offers a variety of automated and streamlined analysis workflows which can be run in their contextual image analysis software StrataQuest:

  • IF Dots App – e.g. for the analysis of FISH experiments (fluorescence mode);
  • RNAScope App – e.g. analysis of dotted structures in brightfield mode;
  • Dots analysis combined with other analysis techniques (e.g. IF Cardio Cell Culture Dots, IHC Small Intestine Dots etc.);
  • And many more – check them out here in TissueGnostics App Center.

 If you cannot find the perfect solution for your research question please contact TissueGnostics. The scientific experts and technical professionals at TissueGnostics will work together with you to design and deliver the best solutions for your research need.


  1. Ratan, Z. A., Zaman, S. B., Mehta, V., Haidere, M. F., Runa, N. J., & Akter, N. (2017). Application of Fluorescence In Situ Hybridization (FISH) Technique for the Detection of Genetic Aberration in Medical Science. Cureus. https://doi.org/10.7759/cureus.1325
  1. ‌Mungenast, F., Fernando, A., Nica, R., Boghiu, B., Lungu, B., Batra, J., & Ecker, R. C. (2021). Next-Generation Digital Histopathology of the Tumor Microenvironment. Genes, 12(4), 538. https://doi.org/10.3390/genes12040538
  1. ‌ (2022). IF Dots APP: FISH. tissuegnostics.com. https://tissuegnostics.com/en/products/imaging-software/170-tissuefaxs-imaging-software

Are you also interested in a demonstrative case study on FISH image analysis?

or in How FISH Image Analysis Factors into Next-Gen Digital Pathology?


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