TissueFAXS
High-Throughput Systems
Automated slide scanning for high-volume workflows and mixed sample runs.
Software Suite 8 is here — DNN tissue detection, label capture with existing cameras, and a redesigned interface with smarter, more intuitive tools.
See what’s new in Version 8 ›
Slide Scanning at Scale
Engineered for core facilities and batch workflows.
TissueFAXS SL, SL Q, and Spectra SL are optimized for high-throughput labs needing fast, flexible imaging. These systems automate the scanning of up to 120 slides per run and accommodate diverse sample types. Magnetic slide grips, automated validation, and mixed-mode compatibility ensure high reliability and minimal downtime. Whether used for brightfield, fluorescence, multispectral, or confocal imaging, SL systems are built for performance at scale.
- Load 120 slides or 60 large-format slides
- Automated loading, scanning, stitching, and validation
- Handle mixed stains and imaging modes
- Optional high-speed confocal and multispectral upgrades
- Barcode & QR label scanning included
Scan More with TissueFAXS Slideloader
Load Once, Scan More
Scan up to 120 slides automatically - perfect for core facilities and large batch imaging workflows.
One-Click Workflow
One-click scanning with automated preview, tissue detection and acquisition, and profile selection.
Flexible by Default
Run mixed sample types and imaging modes in one run, saving time on setup.
Expert support you can count on
You’re supported at every step - with a team that understands your science and setup.
High-Throughput, Flexible and Upgradable. Ideal for core facilities.
TissueFAXS SL is designed for the 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:
Key features of TissueFAXS SL systems
- Automated High-Throughput Imaging
- Optimized Imaging Workflow
- Comprehensive Validation
- Mixed Sample Types
- High-Throughput TMA
- Integrated Label Reader
- Powerful Imaging Software
- Modular and Scalable Design
- Component Flexibility
- Integrated Image Analysis
- Unmatched Expert Support
Automated High-Throughput Imaging
The Slideloader system automates every step of the acquisition process - from slide loading and barcode scanning to whole slide imaging, and image stitching. Three 40-slide magazines support up to 120 standard slides or 60 oversized slides per run. Integrated safety mechanisms, including magnetic slide holders, minimize physical wear and reduce breakage risk. Brightfield, fluorescence, and oil immersion imaging are fully supported in unattended operation.
High-Throughput Imaging Workflow
TissueFAXS Imaging Software includes dedicated automation features for large batch acquisition. Preview, tissue detection, and acquisition can be validated asynchronously to avoid workflow interruptions. Scan profiles and acquisition settings are saved per project, and batch mode allows consecutive projects to run using the same setup. ideal for large cohorts or overnight operation.
Comprehensive Validation Workflows
Validate or adjust tissue detection, preview and/or optimize focus points, and validate regions before or during acquisition - without stopping the batch. The system supports automated or manual review of preview images, and field of view-specific reacquisition is available for refining results. Slide validation status is visible at a glance, making quality control seamless even across high-volume runs.
Mixed Sample Types
TissueFAXS SL supports scanning of mixed slide types and imaging modes in a single batch - including brightfield, fluorescence, oil immersion, and TMA slides. Each slide can be configured with its own acquisition mode, and scan parameters within the same project, allowing labs to run diverse experiments in parallel.
Slide names can be customized manually or imported in bulk from an Excel spreadsheet file, making it easy to maintain consistent sample tracking across large batches.
High-Throughput TMA Workflow
The TMA Workflow is optimized for large-scale TMA scanning, supporting up to 1,000 tissue cores per slide and batch-loading up to 120 slides. This translates to imaging up to 120,000 cores in a single unattended run. The system handles automated layout recognition, barcode-based slide identification, and fully motorized batch acquisition, making it ideal for high-throughput studies and high-demand workflows. Spot selection, grouping, and rescan tools streamline review and quality control, while batch-standardized imaging profiles support consistent, high-throughput acquisition.
Walkaway Automation and Integrated Label Reader
The TissueFAXS SL systems have automation built into every stage of the workflow, everything from barcode or QR code reading to tissue detection and multi-channel acquisition. Slides are scanned using pre-set profiles, and validation steps like preview and region confirmation can also run in the background without interrupting the workflow.
Powerful Imaging Software
TissueFAXS features imaging software designed to support both routine and advanced workflows. Users have full access to all scanning parameters allowing protocols to be precisely tailored and saved as reusable profiles for consistent results. Smart autofocus and Z-stacking with a Z-projection (extended focus) algorithm, improve clarity in thick or uneven samples, resulting in high-quality seamless images.
Integrated virtual slide viewing, annotation tools, and export to open data formats streamline review, sharing, and downstream analysis.
Modular and Scalable Design
TissueFAXS Slide Loader is a versatile high-throughput system capable of imaging up to 120 standard slides or 60 double-sized slides in mixed modes, brightfield and fluorescence. Need to image thicker samples? An additional confocal unit will provide a crisp whole-slide image. Plan a multiplex staining workflow? Multispectral configuration can image up to 8 markers in a single run without channel bleed-through. Thanks to the system flexibility, your TissueFAXS system can grow with your lab.
Objectives, Cameras, Light Sources and Filters
Users can choose from a variety of high-performance cameras for both brightfield and fluorescence imaging; objectives ranging from 1x to 100x in air, water, or oil immersion - with support for up to seven simultaneously mounted; multiple light sources to match specific fluorophore combinations; and filter sets including single-, dual-, and quad-bandpass options.
This component-level flexibility allows configurations to be precisely tailored to specific experimental needs, from routine imaging to advanced multiplexed assays.
Seamless Integration with Quantitative Analysis
The TissueFAXS SL systems are designed for scale - and StrataQuest matches it with robust, batch-ready analysis tools. After scanning up to 120 slides per batch, users can apply preconfigured analysis workflows for nuclei segmentation, tissue classificaton (tumor, stroma etc), and spatial phenotype distribution across the full dataset. This makes it ideal for large-scale translational research, where consistency, automation, and scalability are essential. Barcode-tracked data flows directly into analytics, reducing manual handling and boosting throughput at every stage.
Specialized Expertise, Every Step of the Way
Our systems are backed by a multidisciplinary support team with expertise across hardware configuration, image analysis, and microscopy.
Our application specialists help you define the optimal setup for your imaging needs, while our analysis experts assist in designing and/or refining StrataQuest pipelines tailored to your research. For more advanced needs, engineering and R&D teams are available to develop and integrate custom features or workflows - including new configurations beyond our standard portfolio.
Whether you're scaling your analysis or planning for future upgrades, expert guidance is built into every step.
Upgrade your slideloader with multispectral or confocal modules
High-Throughput Multispectral Imaging
TissueFAXS Spectra SL
- Combines automated 120-slide batch scanning with LCTF-based multispectral imaging.
- Capture more markers in a single scan using multispectral imaging, spectral unmixing and reference libraries.
- Designed for high-content phenotyping and spatial biology.
- Supports mixed sample types, imaging modes and protocols in one run.
- Ideal for core facilities and labs handling large, complex studies.
High-Throughput Confocal Imaging
TissueFAXS SL Q
- Combines high-throughput automation (120 slides) with spinning disk confocal microscopy.
- Acquire high-resolution z-stacks across entire slides with optical sectioning.
- Excellent for thick tissues and subcellular analysis.
- Reduces photobleaching and acquisition time compared to point-scanning systems.
- Perfect for neuroscience, colocalization studies, and spatial research.
Interested in seeing high-throughput TissueFAXS in action?
Maximaize your existing TissueFAXS workflow
Slideloader as an Upgrade Module
All upright configurations of the TissueFAXS system are fully upgradeable with the 120 slide loader module. This upgrade replaces the standard 8-slide stage with a high-capacity automated loader, instantly transforming your system into a high-throughput imaging platform.
While the workflow shifts from semi-automated operation to fully automated batch scanning, it becomes significantly more powerful. The upgrade supports scanning of mixed sample types in one run and seamlessly integrates with existing imaging modes, including brightfield, fluorescence, phase contrast and darkfield.
Explore Our Knowledge Base
Access white papers, application notes and webinars on high-throughput Systems.
Characterizing the Tumor Microenvironment of Colorectal Cancer Patients
What are the Benefits of High-Throughput Imaging Systems for Tissue Analysis?
Ratio of PD-1+ Treg/PD-1+ CTL and Tertiary Lymphoid Structures in Advanced Gastric Cancer
Related Products
TissueFAXS Viewer
Free. Fast. Made for Collaboration.
TissueFAXS Viewer is a free, standalone desktop application for exploring high-resolution virtual slides generated by TissueFAXS systems. It allows researchers and collaborators to navigate brightfield, fluorescence, or multispectral scans, view annotations, and assess results without needing the full imaging setup. It's the ideal tool for sharing and reviewing data across teams.
StrataQuest Image Analysis
Turns imaging data into publication-ready results.
StrataQuest is a powerful analysis platform designed to work seamlessly with TissueFAXS. It transforms high-resolution images into meaningful data, supporting workflows from basic segmentation to AI-driven classification. Scalable and intuitive, it delivers insights into phenotypes, spatial patterns, and tissue architecture across a range of research applications.
- Customizable pipelines for basic & advanced image analysis
- AI-powered nuclei segmentation and tissue classification
- Spatial analysis tools (e.g. neighborhood, distance, clustering)
- Integrated data mining: t-SNE, UMAP, SONG, and more
- Prebuilt analysis apps for oncology, immunology, neurology, and more
- Open format support and direct integration with TissueFAXS systems
Let’s Talk High-Throughput Imaging
Couldn't find the answer to your question? Need assistance?
Whether you're imaging slides, well plates, or complex 3D samples, our team is here to help configure a TissueFAXS system that fits your exact workflow. From hardware recommendations to future upgrade planning, we’ll work with you to design a setup that’s ready for now and built for what’s next.
Technical Specifications
Feature | TissueFAXS SL - All Configurations | ||
|---|---|---|---|
Sample Carrier | Slide Types | glass slides | |
Compatible Glass Slide Formats
| Standard slide: 25 mm x75 mm (1 in × 3 in) | ||
Thickness Cover Glass
|
0.12 mm - 0.17 mm
| ||
Design | Imaging Modes | widefield fluoresence, brightfield*, darkfield*, phase contrast*, polarization*, DIC*, confocal spinning disc imaging (SLQ config.)*, multispectral imaging using LCTF filter (SPECTRA SL config.)* | |
Capacity |
120 standard slides or 60 double sized slides
| ||
Objectives | motorized nosepiece for up to 7 (1x - 100x) air oil or water | ||
Stage |
automated slide loader for up to 120 slides
| ||
Workstation
|
HP Z6, High-performance Windows 11 PC for microscope control and analysis, including 2 x 27 high quality TFT monitors
| ||
Brightfield* |
Light Source |
VIS-LED: Lifetime > 10.000 hours
| |
Color Camera |
Pixelink (CMOS): 2048 x 2048 px; 90.3 fps; up to 63% QE
| ||
Scan Time |
approx. 1.5 min (15 x 15 mm, 20x objective, pure scanning time, 1 focus point)
| ||
Fluorescence
|
Light Source | Options: | |
Monochrome Camera | Options: | ||
FL-Channels | motorized filter wheel, up to 10 positions | ||
Scan Time | Standard FL scan: approx. 9 min (15 x 15 mm, 20x objective, 4 channels, 10ms exposure time, pure scanning time, 1 focus point) | ||
Dimensions
| Measurements | Base: 750 mm x 1050 mm x 1010 mm (29.5 in × 41.3 in × 39.8 in) | |
Weight | Base: 182 kg ± 5% (401.2 lbs ± 5%) | ||
Operation
|
Temperature |
+10 to +30°C (50 to 86°F)
| |
Humidity |
below 40% is recommended; up to 80% without condensation
| ||
Power Consumption |
minimum 500 watts at peak, minimum of two power sockets 110/220 Volts (US/Europe)
| ||
Software
|
Scanning | one click workflow, customizable workflows, access to all scanning parameters, automatic AI based tissue detection, automatic label scanning, HDR and deconvolution**, smart autofocus, z-stacks and z-projections, automatic stitching for seamless whole slide image, dedicated TMA and well-plate workflow, additional in SPECTRA SL: spectral unmixing, reference spectral database, additional in SLQ: 3D visualization | |
Image Export |
aqproj (bioformats), OME tiff, tiff, png, jpg, bmp
| ||
Image Viewer | Free TissueFAXS viewer - download here | ||
Analysis* | AI-based nuclei segmentation, real-time analysis preview, phenotyping and phenotype interactions, proximity measurement tool, AI training center**, dot detection, interactive diagrams, omics explorer**, unlimited multiplexing, library of prebuilt pipelines, data mining tools, customized statistics, versatile data export | ||
*optional
**to come in version 8.1
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