November 28, 2022

How FISH Image Analysis Factors into Next-Gen Digital Pathology

Acquisition, management, dissemination, and interpretation of pathology data, including data and slides, are all included in digital pathology. Whole tissue samples are acquired using slide scanners to produce digital slides, which are high-resolution digital images that can be viewed on a screen. 1

High-throughput automated digital pathology scanners are capable of automatically performing whole slides imaging (WSI) with high magnification (up to 100x) of a high number of slides (eg TissueFAXS SL can scan up to 120 slides). By utilizing specialized digital pathology software tools, digitized slides can be distributed over networks. Automated image analysis methods can also aid the interpretation and quantification of biomarker expression in tissue sections.

What is Digital Pathology?

Digital pathology has more than 100 years of history, starting with the invention of specialized tools to record pictures from the microscope onto photographic plates. Telepathology, or the transmission of microscope images between distant places, has been an idea for nearly 50 years. However, it has only been in the last ten years that digital pathology has truly begun to transition from an analog to an electronic setting. 2

The rapid development of whole-slide imaging (WSI) technology has made it possible to fully integrate digital pathology into pathology workflows, as have improvements in software applications, LIS/LIMS interface, and high-speed networking.

Pathologists may engage, assess, and cooperate quickly, remotely, transparently, and consistently thanks to digital pathology, which boosts productivity and efficiency. Computer-aided diagnosis (CAD), individualized treatment, and improved translational research may someday be a part of the future of digital pathology. 3

Digital Pathology and FISH

In a research or pathology laboratory, efficient workflow management is essential to achieving quick turnaround while maintaining good quality. In both research and digital diagnostic pathology, fluorescence in-situ hybridization analysis (FISH) is the method of choice for identifying single chromosomal abnormalities.

The importance of interphase fluorescence in-situ hybridization (FISH) as a diagnostic and prognostic test in digital pathology has increased. 4 Along with being cost-effective, it enables quick target-oriented examination with results available in a day.

A conventional microscope, with or without a motorized scanning stage, is often used to examine FISH slides. Signal evaluation can be done manually, automatically, or both at the microscope, on a computer screen, or by software-supported algorithms.

Manual quantification of molecular biomarkers can be time-consuming. Therefore companies such as TissueGnostics provides next-generation digital pathology solutions for FISH image analysis or its non-fluorescent analogs, such as CISH, for the automated detection and measurement of target signals. These detection algorithms can easily be optimized to satisfy a range of end-user requirements and are versatile enough to handle single-plex or multiplex analysis. Analyzing the expression of RNA or DNA biomarkers in tissues, cells, or subcellular structures is simple and efficient when using streamlined scanning and analysis workflows like provided by tissue cytometry. TissueGnostics' tissue cytometers are well-known for their outstanding image quality, even with thick tissue sections.

Advantages of whole slide scanning of FISH stainings

  • Acquire whole slide images of the tissue samples to gain a complete picture of the morphology in a flash, even within thick tissue sections (when using confocal whole slide imaging eg TissueFAXS Q);
  • Easily visualize and review entire tissue sections;
  • Remote consultation – telepathology - is possible;
  • Analysis of whole tissue sections;
  • Fully automated and streamlined scanning and analysis workflow.

The benefits of scanning FISH slides significantly outweigh those of traditional fluorescence microscopy examination. New possibilities are made available via storage, sharing, and remote diagnostics and analysis.

TissueGnostics Digital Pathology Solution

TissueGnostics is a solution provider for Precision Medicine and offers fully integrated cutting-edge tissue cytometers. The instruments are available in multiple configurations for whole slide imaging (WSI) in brightfield, fluorescence, multispectral, confocal and high-throughput scanning mode and further allows high-end contextual image analysis.

TissueGnostics provides image analysis solutions for a multitude of research questions. The image analysis software  StrataQuestHistoQuest ,  and  TissueQuest  can be applied eg, to explore the  tumor microenvironment  and/or the  spatial organization of cellular subpopulations , to detect and  quantify fluorescence in situ hybridization (FISH) , to assess different bone structures, or to analysis multiplex IF stainings. 

More information about FISH and related processes can be found online at the TissueGnostics website. If you are interested in learning more about the different types of FISH evaluations, please reach out to a team member of TissueGnostics today.


  1. The Royal College of Pathologists. Digital Pathology. (2020). https://www.rcpath.org/profession/digital-pathology.html
  1. Cooper, L., et al. (2014). Digital Pathology: Data-Intensive Frontier in Medical Imaging. HHS Author Manuscripts. doi: 10.1109/JPROC.2011.2182074
  1. Jahn, S., et al. (2020). Digital Pathology: Advantages, Limitations and Emerging Perspectives. Journal of Clinical Medicine. doi: 10.3390/jcm9113697
  1. Gupta, R., et al. (2018). Fluorescent in situ hybridization in surgical pathology practice. Adv Anat Pathol. https://doi.org/10.1097/PAP.0000000000000194 .
  1. Chea, V., et al. (2021). Optimized workflow for digitalized FISH analysis in pathology. Diagnostic Pathology. https://doi.org/10.1186/s13000-021-01103-5
  1. Biggs, D., et al. (2010). 3D deconvolution microscopy. Curr Protoc Cytom. DOI:  1002/0471142956.cy1219s52

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

or in Understanding the Different Types of FISH Evaluations ?


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+43 1 216 11 90
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