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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

Leishmaniasis parasite detection in cell culture and tissue: Leishmaniasis APP

Leishmania donovani parasites are the causative agents of zoonotic and anthroponotic visceral leishmaniasis. There is no prophylactic vaccine and available drugs are either expensive and/or show significant toxicity, making the research on leishmania biology essential for a detailed understanding of the dispersal of these obligatory-intracellular parasites and their host phagocytes in the skin [1].

The Leishmaniasis APP within TissueGnostics contextual image analysis software, StrataQuest, was designed to assist in immunology research into Leishmaniasis and can be adapted for research on other intracellular parasites. It can be used both on cell cultures and tissue sections. Its main function is to automatically detect parasite stages in cell compartments and quantify them in context with specific immune markers. In this case study, we will show in detail how simple and straightforward the analysis is.

The aim of this project was to detect how many cells are infected by leishmaniasis and the number of leishmaniasis parasites per cell.

The image below shows a mouse skin-draining lymph node stained with DAPI (nucleus, blue).


Nuclei detection based on DAPI staining is one of the most crucial first steps in image analysis; (a) here nuclei are outlined in green. Starting from this, the software defines the whole cell around the nuclei, outlined in yellow for representation (b); (c) detection of parasites inside the cell as shown here as pink dots; (d) combined masks showing cells in yellow and Leishmaniasis parasites in pink.


The obtained data is visualized within StrataQuest using scattergrams. In the example below, (e) cells containing parasites are highlighted in red by selecting them in the proper scattergram (in this case, parasites count vs cell size). The individual cells within an image can be chosen and their exact position in the corresponding scattergram is shown – this is a feature available in StrataQuest called forward connection, especially useful for validation of the selected gates.


In the end, all results with many parameters to choose from can be outputted into common file formats (Excel, PDF, CSV) for further statistical analysis.

However, the power of StrataQuest´s App-based streamlined workflow does not end with cell/parasite detection. For further deciphering of Leishmania life cycle aspects and distribution processes, the parasite load and the status of parasite stages, e.g. “live/dead” can also be evaluated to obtain additive information. The IF Dots APP enables the analysis of FISH-stained leishmaniasis parasites.

A recent paper utilizing StrataQuest´s analysis software showed that programmed death-ligand 1 (PD-L1) expression is predictive of clinical response to treatment in patients with leishmaniasis [2]. If you are interested in performing detailed context-based quantitative analysis, explore the potential of StrataQuest and StrataQuest Apps.



  1. Doehl JSP, Ashwin H, Brown N, Romano A, Carmichael S, Pitchford JW, Kaye PM. Spatial Point Pattern Analysis Identifies Mechanisms Shaping the Skin Parasite Landscape in Leishmania donovani Infection. Front Immunol. 2021 Dec 16;12:795554. doi: 10.3389/fimmu.2021.795554.
  2. Nidhi S. Dey, Paul M. Kaye, Shalindra Ranasinghe. Early reduction in PD-L1 expression predicts faster treatment response in human cutaneous leishmaniasis. October 5, 2021. J Clin Invest. 2021;131(22):e142765. doi.org/10.1172/JCI142765.
  3. TissueGnostics, 2022. White paper. PD-L1 raises new hope in the treatment of cutaneous leishmaniasis.



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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