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

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.


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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