23. January 2023

An Introduction to Spatial Tissue Cytometry

Cytometry encompasses several methods for investigating cells, such as their count, cell cycle state, phenotype, morphology, size etc. The main goal of cytometry is to characterize individual cells. Although flow cytometry is frequently used to obtain this data, the big advantage of tissue cytometry is that the cells are still in their native tissue environment, making it possible to analyze even spatial relationships. This blog post will look at spatial tissue cytometry, its applications, and its advantages.

What is Spatial Tissue Cytometry?

Although a relatively new method, automated tissue cytometry is used for the scanning and analysis of IF/IHC processed tissue samples, TMAs, smears, and cultured cells, thereby characterizing individual cells, as well as metastructures within tissues. Since the cells remain in their native tissue environment, further spatial aspects, such as cell-cell and cell-metastructure associations, can be investigated.

How Does Spatial Tissue Cytometry Work?

Spatial tissue cytometry uses an instrument called a tissue cytometer, which is manufactured with many components. These include sCMOS cameras, high-power LEDs, filters, different objectives, a stage with automatic slide loading, software to enable automated imaging and image analysis to uncover spatial relationships. 

Flow cytometry is often mentioned when discussing tissue cytometry to compare or contrast the methods. As a brief overview, flow cytometry uses complex fluidics systems to measure single cells within a solution. This process is carried out using a laser to scan the cells into a single file. In contrast, tissue cytometers use light microscopy to analyze solid tissue sections.

What are the Advantages of Spatial Tissue Cytometry?

Spatial tissue cytometry provides various benefits when analyzing critical cellular and spatial interactions in their natural environment. Not only can tissue cytometry be used to identify basic cell properties such as their diameter or shape, but scientists can also use them to provide much finer details. 

To summarize, the key advantages of spatial tissue cytometry include:

  • Phenotyping - characterization of a cell;
  • Analyze the functional properties of single cells;
  • Detection of morphological substructures;
  • Assessment of cell interactions with other morphological substructures;
  • Analysis of cell-to-cell interactions.

Spatial Tissue Cytometry with TissueGnostics

At TissueGnostics, we specialize in developing and manufacturing cytometers for various applications. We also develop software for our instruments: HistoQuest for brightfield single cell analysis, TissueQuest for fluorescence single cell analysis, and StrataQuest for both applications with high-end context-based analysis. Look through the wide range of StrataQuest Apps and get inspired by the variety of biomedical image analysis applications. 

TissueGnostics offers a range of tissue cytometers, some of which we have summarized below. If you want a comprehensive list, you can find the variety of TissueGnostics’ cytometers on our product page.


The SPECTRA system can be used for whole slide multispectral fluorescence imaging. It comes with a spectral unmixing engine and is capable of scanning up to 8 markers simultaneously. This system is based on a liquid crystal tunable filter which allows for removal of autofluorescence bleed-through, making the final image clearer for further analysis. This system is also matched with the StrataQuest analysis software. 


The CHROMA is mainly used for automated multispectral fluorescence whole slide scanning, which can be carried out over up to 7 markers simultaneously. This process is enabled by a filter set that has been optimized to eliminate channel bleed-through without scanning lambda stacks.

If you would like more information about spatial tissue cytometry or its applications, please don’t hesitate to contact us.


TissueGnostics GmbH
Taborstraße 10/2/8
1020 Vienna, Austria
+43 1 216 11 90
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