TissueGnostics is a solution provider for Precision Medicine offering fully integrated cutting-edge tissue cytometers including a multitude of configurations from multispectral & high-throughput scanning to contextual tissue cytometry. The goal of TissueGnostics is to bring the same type of phenotypical analysis of single cells from Flow Cytometry into tissue context.

Image Analysis

Image Analysis



Analysis of fluorescent markers

TissueQuest provides three analysis modes:

  • Cell-based (nucleus, cytoplasm, membrane)
  • Stained areas
  • Small dots (e.g. FISH)

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

TissueQuest has importers for the following digital image or slide formats:

  • 3D Histech (.mrxs)
  • Hamamatsu (.ndpi)
  • Zeiss Axio Scan (.czi)
  • Perkin Elmer (.qptiff)
  • Images (.jpeg, .tif, .bmp, .png)
  • Generic Big Tiff
  • OME Tiff

Images to be analysed in TissueQuest must be provided as 8 bit monochrome greyscale images (one image per channel). Overlay (colored multichannel) images can not be analysed.


TissueQuest is integrated into the following TG systems

  • TissueFAXS SL
  • TissueFAXS SL PLUS
  • TissueFAXS Q
  • TissueFAXS PLUS
  • TissueFAXS Fluo
  • TissueFAXS i PLUS
  • TissueFAXS i Fluo

TissueQuest is also available as a standalone software.

TissueQuest 7.0

TissueQuest is an image analysis software for the FACS-like analysis of tissue sections, TMA or cultured cells processed with immunofluorescence. TissueQuest can analyse images from epifluorescence as well as those from Q systems.


New Features in TissueQuest 7.0

The new features of TissueQuest 7.0 include improvements to the analysis workflow, management of multiple diagrams, image visualization, and the user interface. Here are some highlights of 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.
  • 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.
  • TissueQuest 7.0 comes with new visualization modes including pseudo IHC, providing a pathology view (pseudo coloured images) as well as the HDR-like mode (high dynamic range) and a smoothen image function.
  • The 16 bit projects are fully supported in TissueQuest 7.0.
  • New import formats include: OME-TIFF, Olympus VSI, BigTIFF and PreciPoint.
  • The automatic Tissue and TMA Detection function from TissueFAXS and StrataQuest is now also available in TissueQuest.
  • Another new feature is the introduction of the Human Protein Atlas Browser within the TissueQuest software. By simply pressing the Human Protein Atlas Button compare your obtained results to publicly available data.Full 64 bit support will greatly increase the number of samples which can be analysed in one project.


TG introduced Tissue Cytometry technology into image analysis software more than a decade ago with TissueQuest software in its first version. 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“ and „Forward Gating“.


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).


TissueQuest analysis automation

TissueQuests 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 an analysis project and to manually define regions of interest, if any are wanted. Then the template can be loaded, and analysis can be performed automatically.

The template provides:

  • Segmentation settings for all objects to be detected
  • A method for dealing with events in regions of interest (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 

TissueQuest image analysis algorithms

TissueQuest uses algorithms for nuclear and cell compartment segmentation, algorithms for stained area detection as well as algorithms for the detection of dots inside 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.

The images on the right show the segmentation of the nuclei based on DAPI (blue), the cellular segmentation based on Plakoglobin (green) and the assessment of Ki-67+ (red) and Plakoglobin+ (green)  cells. 


The total area algorithm segments stained areas in a sample (indicated in the image below).


The small dot algorithm provides small dot detection ideal for FISH and other applications in which the quantification of small objects within cellular compartments is needed. The image below shows the quantification of FITC and Texas Red FISH dots inside the nuclear compartment.



TissueQuest fully supports the analysis of Tissue Microarrays (TMA) scanned either with TG TissueFAXS systems or those slide scanners for which TissueQuest provides importers. For analysis projects of scans coming from TG 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 TissueQuest.


TissueQuest data export capabilities

TissueQuest provides four modes for the export of analysis data, ranging from simple prefabricated reports for internal presentations to selective data export from all analysis projects from a complete scientific project.

There is a special pathology oriented data export feature for the small dot algorithm data, which has been built according to pathologists requirements for FISH analysis.

All TG data export modes write data to Excel, CSV and PDF formats.


Other TissueQuest features

TissueQuest features include a registration and comparative analysis capability for differently stained consecutive samples. Compare sets provide grouping features for multiple scattergrams and histograms as well as overlaying them.



TissueGnostics has over 1,950 scientific reference publications

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TissueGnostics has over 1,950 scientific reference publications

Learn more ›

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