TissueFAXS SL

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All TissueFAXS upright systems configurations (Fluo, Histo, PLUS) are also available as TissueFAXS SL (Slide Loader) high-throughput systems.

In this configuration, they are additionally equipped with an automatic slide loader and a specially adapted version of the TissueFAXS scanning and image management software.

This software version also includes TGs new SV (Slide Validator) technology.

STissueFAXS SL systems are also available in scan only configurations.


checkTissueFAXS SL systems can be upgraded to the same configurations as the non-loader systems (Histo and Fluo to PLUS, epifluorescence to confocal or high-speed).


  • Fully automated high-throughput scanning - up to 120 slides
  • Option for oversized slides
  • Slide ID Scanner
  • Multi-channel fluorescence & brightfield
  • Extended Focus Imaging & Z-Stacking
  • Quantitative image analysis option
  • Image and metadata storage, management and archiving

TMA Analysis with StrataQuest

Tissue microarrays (TMAs) have proven themselves as a standard molecular clinical diagnosis technique. TMAs are paraffin blocks in which up to 1000 individual tissue cores assembled in array fashion, allowing high-throughput histological analysis.

The TissueFAXS platform including the high-end image analysis solution StrataQuest provides specific workflow to scan and analyze the TMA samples containing multiple regions on one slide. TMA analysis in StrataQuest is available for images acquired in all imaging modalities (multispectral, fluorescence, brightfield).

In the first example, StrataQuest was utilized to analyze a TMA sample stained for hematoxylin (blue) and for E-cadherin present in the cell membranes of epithelial cells (brown). On the original image (a), E-cadherin is shown in brown and nuclei in blue. The aim was to detect the nuclei, the epithelial cells and the membranes of epithelial cells. The challenge with this analysis was that some cells do not contain nuclei.  

TMA Immune status Overview 15 name

Image (b) shows detected nuclei, covered by nuclei mask in light blue. Next only membranes were detected (c), which are shown in green; (d) shows the detection of the whole E-cadherin+ epithelial tissue, also marked in green.


Bild1 cut

In image (e) only cells with nuclei are identified, and the whole cell with the membrane is shown in blue, while the nuclei are covered by the light blue nuclei mask; (f) represents the nuclei in light blue and the total membranes in red.


Bild2 cut

Another example on TMA analysis is our IHC Immune Status in situ APP. Here the task was to develop a streamlined workflow for tissue classification (epithelium, stroma, lymphoid cluster).

Marker positive cells (for CD3+) were identified and spatial analysis was peformed, which would allow for the calculation of how many and which types of cells are located in defined distances from the object of interest (epithelium or lymphoid cluster). In the below example the App was applied to Tissue Microarrays (TMA) of an inflamed bladder.


TMA Immune status Overview 15 cut

One of the most notable features of StrataQuest is the machine learning-based tissue classification. To train the algorithm, the user marks regions assigned to different tissues and trains the classifier on the sample; later this workflow can be used on other samples. The following images represent the outcome of the classifier: (g) epithelium is detected in blue; (h) displays the lymphocyte cluster in light blue. These algorithms (or masks) can be combined to achieve a better visualization: (i) epithelium is displayed in blue, lymphocyte cluster in light blue and stroma in yellow.


TissueClassification cut

Beside the tissue classification itself, StrataQuest is capable of performing proximity analysis. It is possible to define specific proximity ranges; in the following case each range marked by different colors is 20µm. Nuclei detection was applied and CD3+ cells are shown in green, negative cells in yellow; (j) proximity ranges for the epithelium and (k) proximity ranges for the lymphocyte cluster.


TissueClassification2 cut

Apart from visual image analysis, StrataQuest outputs quantitative numbers. This way, it is possible to acquire and validate much more information. For example, StrataQuest can show how many cells are detected in each range: through the establishment of gates, 5.06% of CD3+ cells were found to be very close (in 20 µm range) to the epithelium.


scattergram Tumor Ranges edited cut

Further details about our various products and services can be found on our website. If you are interested in learning more about TissueGnostics solutions for TMA application or other tissue cytometry applications and our related services, please reach out to a member of the TissueGnostics team.


TissueFAXS SL systems are loaded with up to three 40 slide magazines with each magazine containing 20 two slide metal clips for a total of 120 standard slides.

Alternatively, 60 double sized (76 × 52 × 1 mm) slides can also be loaded and scanned, making TissueFAXS SL system one of the few in the market capable of doing this.

The clips are magnetically gripped and moved out to the stage for scanning. In this way, any contact of the slides with moving parts is prevented, safeguarding them against breakage.

TissueFAXS SL systems provide automatic scanning of brightfield and/or fluorescence slides. TMA scanning is supported in all configurations. Combined with TissueGnostics integrated high-speed cameras it provides high-throughput for slides with a speed and versatility in the top range.

TissueFAXS SL is capable of oil immersion scanning.

TissueFAXS SL Configuration


TissueFAXS SL comes with a new version of the TissueFAXS software designed for the perfect handling of the high amount of samples, data validation and storage. There are two main workflows, a simple workflow for one type of slides and an advanced workflow for mixed samples types:


SL Flowchart



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

Microscopy mode

Fluorescence and brightfield scanning (upgrade to TissueFAXS SPECTRA SL or TissueFAXS Q SL)

Compatible Slide Formats

All standard and over-sized slides

Slide Capacity



Up to 7 Objectives (2.5-100x)




Monochrome: sCMOS camera (16-bit, 2048x2048px)
Color: CMOS camera (8-bit, 2048x2048px)

Light Source

Solid-state Light Engine

Tissue Microarray (TMA)


Image Analysis Software

contextual image analysis - StrataQuest, StrataQuest Apps
single cell analysis - TissueQuest and HistoQuest

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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