Full 1
Full 1

single-cell analysis

HistoQuest provides four analysis modes:

  • Cell-based (nucleus, cytoplasm, membrane)
  • Stained areas
  • Small dots (e.g. CISH)
  • Skeleton algorithm for membrane staining

Context-based analysis can be done by manually drawing regions-of-interest. TMAs can be analysed and detected on imported files.

HistoQuest - Features

  • Brightfield image analysis
  • Streamlined workflow
  • Single cell analysis
  • Color separation via spectral unmixing
  • Analyze all types of IHC/HC stainings
  • Analyze tissue sections, TMAs, confluent cells, smears
  • Contextual image analysis by manual ROI definition
  • Nuclear segmentation, total area measurements, dot detection
  • Cytoplasmic and membrane measurements
  • 18 measured metrics per marker
  • Image and data comparison tools

HistoQuest is also available as a standalone software.

HistoQuest 7.1

HistoQuest is a brightfield image analysis software for the FACS-like analysis of tissue sections, TMA or cultured cells processed with immunohistochemical or histochemical stains.


NEW FEATURES in HistoQuest 7.0 & 7.1

The new features of HistoQuest 7 include improvements to the analysis workflow, management of multiple diagrams, image visualization, and the user interface. Here are some highlights of 7.0 & 7.1:

  • 7.1 Nuclear Segmentation using deep learning. It is a particularly useful and simple solution for nuclear segmentation in tissues with extremely high cellular density, weak signal intensity, or high variation in nuclei size and texture.

  • 7.1 Comments from TissueFAXS (slides, regions), including a section for patient information and patient number are available in HistoQuest.

  • 7.1 Export results and analysis masks as BigTiff.

  • 7.1 View diagrams from Statistics Report by double clicking on the result.

  • 7.1 Batch import is now also available for external import sources.

  • 7.0 The new diagrams viewer displays all diagrams associated with a region or sample and allows the user to perform several new tasks, including changing the order of the diagrams via drag and drop, a print preview of the diagrams, set cut-offs, add gates, or show backward connections in the image.

  • 7.0 To further simplify the validation process it is now possible to open multiple samples or regions simultaneously in separate detail windows as well as their raw data, diagram details and diagrams viewer. A dedicated Detail Manager helps to stay organized.

  • 7.0 comes with the new smoothen image function, for visual improvement of the image and new import formats including OME-TIFF, Olympus VSI, BigTIFF and PreciPoint

  • 7.0 Another new feature is the introduction of the Human Protein Atlas Browser within our HistoQuest software. By simply pressing the Human Protein Atlas Button compare your obtained results to publicly available data.




TissueGnostics introduced Tissue Cytometry technology into image analysis software more than a decade ago. While, at a first look, it may appear to be just another form of displaying data, there is much more to it. Combined with segmentation images it is also a simple and intuitive tool to visually validate results. TG calls this "Backward Gating". Backward gating can be done for any measured parameter on histograms and scattergrams. The following examples demonstrate the versatility of backward gating. In the left image backward gating is used to visualise cells in which the HER2/neu staining has a closure angle of more than 180 degrees. In the right image backward gating is used on segmented nuclei positive for Ki-67. 

Backward gating Histoquest

Morphological filtering using Tissue Cytometry technology combined with appropriate planning of the analysis provides a highly flexible and capable instrument for extracting specific data from a sample (see image below).

Tissue Cytometry technology

HistoQuest analysis automation

HistoQuests fully automated template-based analysis is optimised for clinical routine and research applications and allows complete walk away operation.

The user just has to load samples into the software and to decide whether they want the samples to beautomatically detected (in which case analysis will start immediately), whether they want to be able to interfere with the automatic region detection (with validation) or whether they want to manually define regions-of.interest.


A template provides:

  • Segmentation settings for all objects to be detected
  • A method for dealing with events in ROI
  • Markers
  • Diagrams from the first sample of the project from which the template was saved
  • Statistics report settings
  • Simple report settings
  • Small dots settings 



HistoQuest image analysis algorithms

HistoQuest AlgorithmBrightfield images need to be separated into images according to their color components, HistoQuest provides two algorithms for color separation. 

The first one automatically detects and separates two colors and an optional third one. The second color separation algorithm is semi-manual (using a color picker) and separates an unlimited amount of colors with great control and precision.

HistoQuest uses algorithms for nuclear and cell compartment segmentation. It also provides an algorithm for stained area detection as well as algorithms for the detection of dots inside of already detected cell compartments.




The nuclear segmentation algorithm is highly efficient in difficult situations in tissue and can be set with two values only - mean nuclear size and nuclear channel background threshhold. The cell compartment algorithm provides a large amount of flexibility with a few simple settings (yellow outline = segmented nuclei, blue outline = nuclei positive for DAB or cytoplasm positive for Permanent Red marker). The total area algorithm segments stained areas in a sample.


 The dot algorithm provides small dot detection ideal for CISH, ISH and other applications in which the quantification of small objects within cellular compartments is needed. The images below show the quantification of EGFR RNA dots inside of the nuclear compartment. Simple context-based analysis can easily be done in HistoQuest by using manual region tools. Drawing the regions takes a negligible amount of time and provides data for epithelial areas and stroma separately in this example. The skeleton algorithm permits the detection of membrane stainings.

quantification of FITC and Texas Red FISH dots inside of the nuclear compartment.


Analysis Support

HistoQuest fully supports the analysis of Tissue Microarrays (TMA) scanned either with TissueFAXS systems or those slide scanners for which HistoQuest provides importers. For analysis projects of scans coming from TissueFAXS systems the autodetected TMA regions will be imported. For scans imported from other scanning systems without detected regions the TMA autodetection feature is also available in HistoQuest.



 HistoQuest 7.1TissueQuest 7.1 StrataQuest 7.1
Available as a standalone software
Analyze tissue sections, TMAs, confluent cells, smears
Flourescence image analysis  
Brightfield image analysis  
Single cell analysis, total area measurements, dot detection (FISH, CISH, RNAScope), cytoplasmatic and membrane measurements
Contextual image analysis by manual ROI definition
Deep-learning nuclear segmentation
Machine-learning tissue classifier, metastructure detection, automated contextual tissue cytometry, proximity & distance measurements, Spatial relationships & tissue microenvironment analysis    
Highly customizable analysis development    
Apps with predefined analysis solutions    
Analysis of confocal/multispectral and time-lapse projects    


Operating System Windows 10 System
Platform compatibility TissueFAXS platform (.sqproj), StrataFAXS II (.vmic), Precipoint (.vmic, .gtif), OME-Tiff, Generic Big Tiff, Images (.jpeg, .tif, .bmp, .png), 3D Histech (.mrxs), Hamamatsu (.ndpi), Zeiss Axio Scan (.czi), Yokogawa, Aperio (.svs), Leica (.scn), Keyence, Perkin Elmer (.qptiff)
Export file compatibility Matlab, Python, ImageJ, FIJI, FCS express, most external command line engines


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