01. September 2022

What is Spatial Phenotyping?

The context through which biomedical scientists analyze cellular phenotypes within tissues determines the type of information that will come out of the laboratory. Spatial biology is one such context in which biological studies can be conducted and is particularly impactful in immunological research because this data could lead to clinical outcomes. Spatial biology examines not only the type of cells within a tissue but also delves into questions surrounding cell population locations, gene and biomarker expression patterns, and cell dynamics within the native tissue microenvironment [1]. Spatial phenotyping encompasses the advanced imaging methodology used to answer this diverse array of spatial biology questions.

This blogpost will provide a brief introduction to spatial phenotyping. Here, we will explore the basics of spatial phenotyping, how it is conducted, why it is important, and spotlight an example of how it can be used in immunotherapy to specifically conduct spatial phenotyping of the tumour microenvironment (TIME).

How to Conduct Spatial Phenotyping

The basic process of conducting spatial phenotyping involves the preparation and staining of tissue sections for multiple markers. Spatial phenotyping requires advanced tissue cytometry technology that can first perform whole-slide acquisition, and second an in-depth characterization of the cellular phenotypes in an understandable and time-efficient manner. While the traditional method of flow cytometry allows for multiple biomarkers to be studied simultaneously, it does not consider the native microenvironment of the cell it exists within, which yields valuable information [2].

However, innovative screening technology resolves this challenge. For example, the medtech company TissueGnostics, has developed the TissueFAXS CHROMA for High-Speed Multispectral Imaging, a part of their TissueFAXS product line [3]. This innovative platform is designed to efficiently conduct automated fluorescence whole slide scanning for up to seven biomarkers. As follow up the power of TissueGnostics’ high-end image analysis solution StrataQuest can be utilized to perform single cell and contextual image analysis as well as spatial phenotyping [4]. This expands the potential of useful knowledge biomedical scientists can extract from the exceedingly complex tissue sections.

Spatial Phenotyping in Immunotherapy and Studying the Tumor Microenvironment

The goal of spatial phenotyping is to characterize phenotypic and functional information of cell populations in a spatial context. For example, spatial phenotyping can reveal dynamics within the cell and tissue microenvironment through the scanning and identification of various cellular phenotypes within tissue sections, biopsies, and organoids; the purpose of this is to identify therapeutic targets to help the immune system combat disease [4]. This information is especially useful in supporting clinical decisions, making spatial phenotyping significant to immunotherapy.

One instance of this is spatial phenotyping of the tumor microenvironment, which can reveal physical and functional data about tumors. This can help investigators unravel how to treat them, and use this information in predicting clinical responses to treatments [5]. By understanding the immune reaction on site of the tumor, informed decisions and predictions can be made about cancer therapeutics.

Spatial Phenotyping with TissueGnostics
TissueGnostics is a leading life sciences solutions provider that is experienced in tissue cytometry solutions such as spatial phenotyping. We provide high-performing products equipped with automation and deep learning to meet tumor microenvironment analysis needs.

Collaborating with us has many benefits to the research workflow, including using a line of TissueFAXS products featuring advanced spatial phenotyping capabilities. Our team deliver the best solutions designed with the scientific priorities of accurate, detailed, and replicable data acquisition of the tumor microenvironment in mind. Further details about the diverse array of products and services we offer, can also be found on our website.

If you are interested in learning more information about spatial phenotyping and our related products, please reach out to a member of the TissueGnostics team as soon as possible.


  1. TissueGnostics (2019). Immune Cell Microenvironment | Complex Characterization. [online] Tissuegnostics.com. Available at: https://tissuegnostics.com/white-papers-phenotyping.
  2. TissueGnostics (2022). High-Speed | Multispectral Tissue Cytometer | Supplier. [online] Tissuegnostics.com. Available at: https://tissuegnostics.com/products/multispectral-cytometer/tissuefaxs-chroma.
  3. TissueGnostics (2019). White Paper Immune Cell Phenotyping. [online] Tissuegnostics.com. Available at: https://tissuegnostics.com/46-white-papers/230-white-papers-phenotyping.
  4. Science.org. (2021). Spatial phenotyping of the tumor microenvironment: Implications for immunotherapy. [online] Available at: https://www.science.org/content/webinar/spatial-phenotyping-tumor-microenvironment-implications-immunotherapy.

Are you also interested in Understanding the Tumour Immune Microenvironment?

or in How to Carry Out Complex Characterization of the Tissue Microenvironment?


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