09. October 2023

Revolutionizing Tissue Analysis: Image-Based Cytometry

Image-based cytometry is rapidly revolutionizing tissue analysis. It is a technique that combines fluorescent microscopy and features of conventional flow cytometry to rapidly characterize individual cell populations in the native tissue environment. This process provides valuable insights into cell characteristics including morphological parameters, marker expression, phenotypes, etc. Image-based cytometry is crucial to applications such as DNA analysis, protein expression, and tumor classification, among many others. 

In this blog post we will discuss the importance of tissue analysis in research and clinical applications, look into image-based cytometry techniques, and discuss the role of deep learning and artificial intelligence in advancing this field. We will also highlight the advantages of image-based cytometry and explore its applications in pathology, oncology research, and future possibilities.

Image-Based Cytometry Techniques

There are several image-based cytometry techniques that are used in scientific research to study cells and tissue, including the two powerful methods, flow cytometry and tissue cytometry.

Flow Cytometry

Flow cytometry is a well-established technique that has been utilized in life science research and diagnostics for over five decades. It allows for the rapid quantification of molecules expressed by single cells and has evolved to enable the simultaneous staining of up to 20 or more markers. Common applications of flow cytometry include cell-cycle analysis, cell sorting, immunophenotyping, and serological testing.1

However, some drawbacks of flow cytometry are that it only works on cells in suspension and cellular markers can be damaged during the lengthy process of enzymatic digestion.  As a result, another analytical method was developed: tissue cytometry.

Tissue Cytometry

This method is used to quickly and precisely characterize single cells within solid tissue sections on a slide and precisely analyze multiple markers. It can be used with a range of samples, such as cell culture monolayers, cryo-cut sections, and paraffin-embedded tissue.

Other applications that benefit from tissue cytometry include analyzing the functional properties of single cells, characterizing cells, or identifying morphological multicellular substructures (such as blood vessels, tumor, stroma, glands, etc.) and their interactions with other substructures or phenotypes.

Tissue cytometry is an ideal technique for phenotypic characterization, which is crucial for understanding the mechanisms behind certain diseases and developing a specific treatment. This method also plays an important role in precision medicine and improving individualized healthcare for patients.

Tissue Cytometry Vs. Flow Cytometry: What's the Difference?

Importance of Tissue Analysis in Research and Clinical Applications

Tissue analysis is a widely used technique in both clinical and research applications, as it enables scientists to gain a deeper understanding of diseases and develop effective diagnostic and treatment strategies. Traditional methods of tissue analysis require the manual examination of tissue samples under a microscope, which is both subjective and time-consuming. 

Image-based cytometry offers a more efficient and objective approach to analyzing tissue samples by enabling an automated method of whole-slide imaging, image segmentation, and analysis. Automating image segmentation and analysis significantly reduces the time required for data collection and interpretation when a high number of markers are stained. Secondly, integrating artificial intelligence enhances image-based cytometry, enabling the discovery of new patterns and insights within biological systems. This integration improves the accuracy and efficiency of data analysis, leading to more robust research outcomes.

TissueGnostics (TG) has developed several streamlined solutions for biomedical imaging and image analysis, including fully automated systems that undertake processes such as whole slide scanning as well as high-end image analysis, which then enables the detection of multicellular structures, quantifying marker expressions, and more. 

Applications and Future Directions

Image-based cytometry finds applications in various fields, particularly pathology, immunology, and oncology research. It provides researchers with a powerful tool to study disease progression and identify molecular drivers within tumors and the host immune response. By analyzing tissue samples at a cellular level, image-based cytometry contributes to personalized medicine and the development of targeted therapies.


Immunophenotyping is used to diagnose diseases by exploring the molecular markers on the cells to define the differences and categorize the subpopulations. This is carried out with flow cytometry or immunohistochemistry on cells or tissue sections placed on slides. In next-generation tissue cytometry, TissueGnostics have developed the TissueFAXS® platform, which uses, among others, high-resolution IF multi-channel microscopy and automated whole slide imaging to offer a high analytical accuracy of phenotypic cell identification

Modern Oncology

Image-based cytometry techniques are being developed in tandem with advanced AI, creating new pathways for diagnosing cancer. The benefits of using image-based cytometry include its rapid optical imaging, identifying specific immune cells, and that it has a low false-positive rate.

Tissue Analysis with TissueGnostics

Image-based cytometry has revolutionized tissue analysis by providing rapid, detailed, and high-throughput characterization of individual cells. The integration of deep learning and artificial intelligence has further enhanced the capabilities of image-based cytometry, leading to breakthroughs in research and diagnostics in various scientific disciplines. With its numerous advantages and wide-ranging applications, image-based cytometry is poised to play a vital role in advancing our understanding of biological systems and driving innovations in pathology, oncology research, and beyond.

TissueGnostics has developed a range of cytometry instruments to overcome various imaging issues. We offer the TissueFAXS system range, providing fully automated systems that combine high-quality optics and image analysis software to enable a range of biomedical imaging applications. In addition, we have three image software solutions: TissueQuest for fluorescence image analysis, HistoQuest for brightfield image analysis, and StrataQuest for multicellular contextual tissue analysis, for both brightfield and fluorescence images.

Contact TissueGnostics today to learn more about how we are revolutionizing tissue analysis through cytometry and deep learning.


References and Further Reading




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