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High-Speed Multispectral Tissue Cytometer

TissueFAXS CHROMA specializes in automated multispectral fluorescence whole slide scanning for up to 7 markers at a time made possible by an optimized filter set eliminating channel bleed through. This cost-effective high-speed slide scanner reaches its full potential when combined with single cell and contextual image analysis. This platform is a holistic solution for cellular phenotyping and in-depth tissue microenvironment characterization of IF processed tissue sections, TMAs, and cells on standard and oversized slides.



  • High resolution (16bit) multispectral fluorescence imaging
  • Simultaneous acquisition of up to 7 markers
  • Optimized for highest scanning speeds
  • In-depth cell/tissue microenvironment characterization
  • High-content phenotyping
  • Whole slide imaging
  • 8 slide capacity with continuous batch mode scanning
  • Supports scanning of tissue sections, biopsies, TMAs, fixed & cultured cells, and organoids
  • One click automation
  • Z stacking & extended focus for increased image quality
  • Quantitative image analysis supported by deep learning and machine learning


TissueFAXS CHROMA provides high-speed multispectral imaging and is made possible by a customized set of SpectraSplit filters. This specialized set of filters is optimized for a wide range of dyes with the appropriate excitation/emission spectra. This technology minimizes channel bleed-through passively and therefore represents a cost-effective alternative to the liquid crystal tuneable filter, which relies on lambda stacking and spectral unmixing of overlapping emission spectra. The acquisition of lambda stacks and spectral unmixing are time consuming and data-heavy processes. TissueFAXS CHROMA focuses on increasing sample throughput by minimizing multispectral scanning speeds without compromising spectral specificity and data integrity.

  • SpectraSplit DAPI
  • SpectraSplit 440 (Opal Polaris 480)
  • SpectraSplit 488 (AF488, FITC, Opal 520)
  • SpectraSplit Cy3 (AF555, Opal 570)
  • SpectraSplit 594 (AF594, TexasRed, Opal 620)
  • SpectraSplit 647 (AF647, Cy5, Opal 690)
  • SpectraSplit 750 (AF750, Cy7, Opal Polaris 780)

TissueFAXS CHROMA is an upright system with an 8 slide stage, high quality Zeiss objectives, state-of-the-art monochrome camera, high power illumination device, TissueFAXS scanning and management software.


TF Chroma Technology

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:



Upright microscope, modular (Microscope, Cameras, Light-source, PC with 2 Monitors)

Microscopy mode

Multispectral fluorescence, widefield fluorescence

Compatible Slide Formats

All standard and over-sized slides

Slide Capacity

8 (standard configuration)


Up to 7 Objectives (2.5-100x)




Monochrome: sCMOS camera (16-bit, 2048x2048)

Light Source

Solid-state broadband light engine

Tissue Microarray (TMA)


Image Analysis Software

contextual image analysis - StrataQuest Fluo, StrataQuest Apps
single cell analysis - TissueQuest

Supported Image Formats



TissueFAXS Viewer: Integrated, stand-alone freeware


TissueGnostics GmbH
Taborstraße 10/2/8
1020 Vienna, Austria
+43 1 216 11 90
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