StrataQuest
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.

IF Dots App: Analysis of FISH

Fluorescence in situ hybridization (FISH) has been routinely used for decades in research and clinics to rapidly identify potential genetical changes within cells. This case study shows how TissueGnostics’ image analysis solution StrataQuest can be applied to evaluate FISH stainings. The most streamlined solution, the IF Dots App (runs within StrataQuest), can be applied to any analysis of dot-sized objects within the nuclei. Depending on the research needs, the following analysis can be combined with any other kind of analysis including AI-based tissue classification, phenotyping, spatial analysis, etc.

The aim of the following case study was to (i) identify individual nuclei and (ii) to assess how many FISH dots per individual nuclei are present.

The image below shows an overview of a triple staining: the nucleus stained by DAPI (blue), and two FISH markers, the housekeeping gene (green), and HER2/neu (red).

IF Dots original 95

The automated analysis starts with nuclei segmentation (a), where nuclei are identified by the intensity of the DAPI staining (nuclei are marked by the green outline). In the next step, the FISH dots are detected: in red the housekeeping gene in FITC channel (b) and in yellow for the HER2/neu in Acridine channel (c). Then these masks can be combined, as seen in (d).

IF Dots min

For further visualization of the analysis results, StrataQuest outputs the data in scattergrams. In the example below, the number of Acridine dots per nucleus (y-axis) is plotted against the FITC dots per nucleus (x-axis). The identified nuclei were gated for the condition “2 acridine dots per nuclei”, where the number of FITC dots can vary, and selected cells are shown in red contour via backward connection. Scattergrams showing the number of detected nuclei with each dot number combination are useful, especially with the Heat Map function enabled (bottom) which indicates those groups with a higher quantity of nuclei. To gain quantitative data for statistical analysis, the results can be immediately exported to Excel, CSV, and PDF formats.

IF Dots 2 min

FISH analysis is only one example of StrataQuest´s capabilities. If you are interested in how StrataQuest streamlined image analysis solution can enhance your research today, please reach out to a TissueGnostics team member for a demonstration.

Get to know more about FISH applications combined with TissueGnostics solutions in our blog posts:

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.

HistoQuest 7.1

TissueQuest 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

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