Full 1
HISTOquest
Brightfield TISSUE CYTOMETRY
Full 1

HistoQuest
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
THE EASY SOLUTION FOR BRIGHTFIELD ANALYSIS

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.

HistoQuest

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.

 

DetailManager

Adipocyte App: Measurement of Cellular Size of Adipocytes

The StrataQuest-based Adipocyte App was applied to this sample with the aim to automatically detect (i) the number, (ii) the size, and (iii) the diameter of adipocytes within the given fat tissue. The challenge of analyzing the adipocytes is that the nuclei cannot be detected properly since they are either usually washed away during the H&E staining process, or are not visible. Therefore, the App detects the adipocytes using the membranes of the cells.

(a) Shows fat tissue stained with hematoxylin & eosin (H&E). The App first detects the membranes of the adipocytes and minor membrane tears are automatically closed (b).  To detect the individual cells without nuclei, the App uses the detected membranes as a starting point and defines the cell by its distance from the membrane (c). Here the final result of cell detection is shown (d), cells are labeled in different colors for visualization purposes.

The App automatically eliminates adipocytes on the borders from the analysis which may influence the proper outcome of the analysis.

 IF_Tumor_Foci_Angio_overview-min.png

The results of the analysis are visualized in histograms and scattergrams. As shown in the scattergram below, the cells can be grouped according to their diameter (e) or (f) size.

IF_Tumor_Foci_Angio_panel-min.png

By selecting a gate of interest within the scattergram and using the backward connection feature, the cells from the selected gate are viewed directly in the sample in their native tissue environment (g). In this case, cells with diameters of 120µm to 129µm are shown in red.

IF_Tumor_Foci_Angio_scattergram.png

The gained measurements can be exported from StrataQuest in CSV and /or Excel format.

StrataQuest Apps offer a streamlined and easy workflow for analyzing your samples. Look through our StrataQuest Apps and get inspired by the variety of biomedical image analysis applications. If you cannot find the perfect solution for your research question, please contact us. TissueGnostics offers the development of customized Apps for your specific analysis needs.

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.

 

 

Nuc-and-Cyto-Segm

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.

 

TISSUE MICROARRAY
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.

microarray

CAPABILITIES

 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    

PROPERTIES

  
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

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