Full 1
Full 1

Context-based Analysis

StrataQuest is TGs most advanced image processing solution for both brightfield and fluorescence images. It provides features such as detection of tissue structures, nuclei/cells, cellular compartments, measurement of proximities and spatial relationships on a digital slide. It integrates detected objects into detailed context-based quantitative analysis.

There are over 50 StrataQuest Apps which can be used for automated analysis and the number is constantly growing.


StrataQuest - features

  • Brightfield and fluorescence image analysis
  • Deep-learning nuclear segmentation
  • Machine-learning tissue classifier 
  • Contextual tissue cytometry
  • Proximity / distance measurements
  • Spatial relationships / tissue microenvironment analysis
  • Metastructure detection
  • Single-cell analysis
  • Spectral unmixing
  • Image crops feature for scattergrams
  • Z-stack and time-lapse analysis
  • Highly customizable analysis development
  • Apps with predefined analysis solutions
  • High degree of image pre-processing
  • Integrated statistics
  • Image and data comparison tools

StrataQuest is also available as a standalone software.

StrataQuest Apps
The Easy Solution For High-Level Image Analysis 

A StrataQuest App is simply an analysis solution for a specific task. It is complete up to the point of providing the specific analysis results ready to be exported to, e.g., Excel or CSV formats. This is complemented by an export function for all images from the software. The core feature of an App is a simplified, tabbed "Easy Mode" user interface. While an App is meant to be run by simply clicking the "Analyse" button, the interface allows the user to make adaptations to sample/staining variance if necessary. TGs decade-long experience in providing analysis solutions to the biosciences market has taught that vaunted "only one click" products work - but only on the textbook quality image on which they are presented.

SQ userInferface

StrataQUEST APP Selection

New Features in StrataQuest 7.0 & 7.1

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

  • 7.1 Introduction of “Quick Actions”: This is a new StrataQuest feature used to combine frequent operations in a single action. There are multiple Quick Actions types based on the context from which they are triggered (Layer, Engine, Diagram (quadrants and gates)).
  • 7.1 New engines: improved “Remove Objects”, “Membrane Measurements”, “Events centroids”, “Distance Map – inside”, “Assign classes to objects”, “Background Removal”, etc.
  • 7.1 Image only feature allows visualizing only the image within the viewer in a full screen.
  • 7.1 New intuitive Tissue Detection parameters/layout.
  • 7.1 Improved interface for: “Dots Measurement”, “Membrane Measurement”, “Virtual Channel”
  • 7.1 Show diagram button: allows showing/hiding the Diagrams section.
  • 7.0 Improved image display settings: a new channel histogram has been added for easier signal detection (image on the right). Lower and upper thresholds can be adjusted more intuitively by drag and drop.
  • 7.0 Nuclear Segmentation Engine can now be used in real time, change parameters and see their effect live.
  • 7.0 New deep learning-based Nuclear Segmentation Engine for a more precise nuclei detection.
  • 7.0 New engines for workflow simplification: Tissue Detection Engine, Background Removal Engine, Proximity Areas Engine, Projection Engine.
  • 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.
  • 7.0 Improved function and/or user interface of various SQ tools (Layers Editor, Image Types, Image display settings, Manage Diagrams, Manage Gates, Basic Operations Engine, Dot detection engines, scoring function…).
  • 7.0 Z-stacks and Time-lapse are now visible, and individual stacks and time frames can be analyzed.
  • 7.0 Our powerful Classifier Engine allows to distinguish morphologically different regions (e.g tumor and stroma) by simply marking a few characteristic areas.
    7.0 TissueFAXS integrated automatic scanning (dual TF-SQ multitask workflow).
  • Optionally, 7.0 comes with a new image crops feature for scattergrams. Instead of dots, crops of the analyzed objects can be displayed in the scattergram.
  • 7.0 Data compare sets feature from HiQ and TQ is now also available in SQ.
  • 7.0 Easy to use Lambda Stack Navigation function.
  • 7.0 Another new feature is the introduction of the Human Protein Atlas Browser within our StrataQuest software. By simply pressing the Human Protein Atlas Button compare your obtained results to publicly available data.
  • 7.0 New import formats: OME-TIFF, Olympus VSI, BigTIFF and PreciPoint.





Dual TF-SQ multi-task Workflow

This workflow displays the power of TissueFAXS (TF) and StrataQuest (SQ) operating together as fully automated system. This highly versatile workflow is based on the modular TissueFAXS systems and the advanced image processing capabilities of StrataQuest.


  StrataQuest Multi Task Workflow


 HistoQuest 7.1TissueQuest 7.1StrataQuest 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
This email address is being protected from spambots. You need JavaScript enabled to view it.

We use cookies on our website. Some of them are essential for the operation of the site, while others help us to improve this site and the user experience (tracking cookies).
You can decide for yourself whether you want to allow cookies or not. Please note that if you reject them, you may not be able to use all the functionalities of the site.