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

IHC 2 APP: Ki-67 Nuclear Staining Analysis

The nuclear protein Ki-67 is an established cell proliferation marker in research and clinics. Its staining and evaluation in tissue sections is an integral part of cancer diagnosis and prognosis.  Automated quantitative analysis of marker expression can provide a valuable supplement to visual evaluation. The IHC2 App is among the StrataQuest easiest-to-use analysis Apps and requires very little preparation time. This streamlined one-click analysis solution allows single cell detection, including the quantification of one additional marker within brightfield images.

The aim of the following case study was to assess (i) the total number of cells as well as (ii) the number and % of Ki-67 positive cells. (a) shows colon tissue stained for hematoxylin (blue) to detect the nuclei and Ki-67 (brown).

The first step of brightfield analysis is color separation. Using the color separation engine (b), the blue marker is automatically separated from the brown marker, as they are shown in grayscale images below.

The second step is the automatic identification of nuclei based on hematoxylin and Ki-67 staining. Since Ki-67 is located in the nuclei and is also covering the hematoxylin staining there, the nuclei can be detected from both markers. Analysis masks provide visual control of the correctness of the nuclear segmentation – here the nuclei are outlined in green (c).

After setting a cut-off on the intensity of the Ki-67 marker in the corresponding scattergram, Ki-67 positive cells are shown with a red outline (d).

IF Dots original 95

Backward connection allows to check cells of interest separately on the corresponding scattergram (e), for example, for checking a possible outlier. The scattergram on the example is plotted for mean Ki-67 intensity vs nuclei size. The results can be exported in common CSV or Excel formats.

 

IF Dots min

Nuclear segmentation, as well as marker detection, is only one of the possibilities of the streamlined analysis solution available for StrataQuest. Get inspired by other analysis solutions in our StrataQuest App Center. Our team would also be glad to develop a personalized solution for you.

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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