TissueFAXS Imaging Suite

TissueFAXS Imaging Suite is a microscopy acquisition and image management software platform developed by TissueGnostics, designed to support both routine scanning workflows and complex, multi-modal imaging tasks. It is suited for research laboratories, core facilities, and clinical research environments working with tissue sections, tissue microarrays (TMAs), well plates, and live-cell cultures. Version 8 of the suite introduces deep neural network (DNN)-based tissue detection, simplified slide label capture, and a redesigned user interface.

The software runs across upright and inverted TissueFAXS hardware configurations and integrates directly with StrataQuest, TissueGnostics' quantitative image analysis platform, enabling a continuous workflow from image acquisition through to spatial and cellular analysis without intermediate file conversion steps.

Whole Slide Imaging and Stitching

• Performs real-time stitching during scanning, assembling individual fields of view into a single continuous image using a validated stitching algorithm.
• Users have access to stitching parameters for adjustment and optimization across different sample types.
• Individual out-of-focus fields of view can be selectively rescanned with a modified z-position without repeating the full scan.

Customizable Scanning Workflows

• Full access to scanning parameters including focus strategy, exposure time, lamp intensity, Z-stack depth, and field-of-view overlap.
• Predefined camera profiles provide optimized starting points for common imaging needs.
• All settings can be saved as custom profiles to support consistent, repeatable acquisition across users and experiments.

HDR Imaging

• High-dynamic range imaging uses 16-bit monochrome acquisition to preserve signal quality across the full tissue area.
• Captures detail in both bright and dim regions, which is particularly useful in fluorescence applications where marker expression levels vary widely.

Smart Autofocus

• Three predefined autofocus modes — Speed, Balanced, and Quality — provide starting points that can be further customized.
• Supports both focal-plane scanning (single-axis movement) and matrix-based focus evaluation (grid of focus points).
• Focus points can be manually repositioned as needed.

Z-Stacking and Z-Projection

• Captures Z-stacks and projects them into sharp 2D images using a proprietary extended focus algorithm.
• Each pixel in the final image is sourced from the sharpest Z-plane, reducing background noise amplification.
• Improves imaging quality for thicker or uneven samples.

Virtual Slide Viewer and Annotation Tools

• Virtual slides are composed of stitched fields of view, providing a continuous high-resolution view of the entire sample.
• A smart caching system dynamically preloads image data during panning and zooming to support responsive navigation across large scans.
• Interactive annotation tools allow users to mark regions of interest, add notes, and export annotations for collaboration, reporting, or downstream analysis.
• Visualization options include fluorescence channel overlays for reviewing multiplexed tissue data.

Walkaway Automation and Label Reading

• Supports fully automated, unattended scanning workflows including automated tissue detection, channel-specific autofocus, custom acquisition profiles, and batch processing.
• Barcode and QR code reading enables automatic sample identification and metadata assignment during acquisition.
• Walk-away automation is standard across all upright and inverted TissueFAXS configurations.

TMA and Well Plate Workflows

• Dedicated scanning modes for tissue microarrays (TMAs) and multiwell plates, supporting up to 1,000 tissue cores and 6- to 96-well formats.
• Features include automated layout detection, per-core and per-well autofocus, and channel-specific acquisition settings.
• Tools for defining and editing TMA blocks and spots, including placeholder management and custom naming schemes.
• Individual TMAs or wells can be selectively rescanned with modified parameters such as higher magnification or additional channels.

Open Data Format Support

• Supports export to OME-TIFF, BigTIFF, TIFF, PNG, JPG, and BMP formats.
• OME-TIFF supports integration into FAIR data workflows (findability, accessibility, interoperability, and reusability).
• Open format compatibility facilitates data sharing, long-term storage, and compliance with institutional or publication requirements.

Live-Cell and Time-Lapse Imaging

• Supports time-lapse acquisition for monitoring dynamic changes in live-cell cultures over time.
• Users can define the number of acquisition cycles and set custom intervals ranging from seconds to days across single or multiple regions of interest.
• Acquisition settings including time intervals and run counts are recorded for traceability.
• Default template saving is supported for frequently used live-cell protocols.
• Applicable for observing cell migration, division, or drug response.

Integration with StrataQuest Analysis Software

• Acquired images move directly into StrataQuest for quantitative analysis without file conversion or additional export steps.
• Supports applications including basic IHC analysis, multi-channel spatial analysis, cell phenotyping, tissue segmentation, and subcellular dot quantification.
• A feedback scanning capability (planned for version 8.1) will allow analysis results from StrataQuest to trigger targeted deeper imaging based on detected patterns or features, supporting workflows such as bone marrow analysis, rare event detection, and targeted phenotyping.

Key Upgrades in Suite 8

• DNN Tissue Detection: A deep neural network-based tissue detection method provides more accurate identification of tissue areas, supplementing threshold-based detection and reducing manual intervention in high-throughput or complex sample workflows.
• Easy Slide Label Registration: Label capture is now possible using the system's existing camera, removing the need for a dedicated label camera. New options support exporting label data alongside images.
• Redesigned User Interface: Includes an improved Layer Editor, an Image and Category Toolbar for verification, an Object Inspector with raw data access, a customizable workspace with draggable panels, a new Project Database view with thumbnails and slide previews, and integrated Bio-Formats import for broader file compatibility.

TissueFAXS Viewer

• A free, standalone desktop application for navigating high-resolution virtual slides generated by TissueFAXS systems.
• Supports brightfield, fluorescence, confocal, and multispectral scans.
• Allows viewing of annotations and review of results without requiring the full imaging system.
• Intended for sharing and reviewing data across research teams and collaborators.

TissueFAXS Imaging Suite is compatible with a range of TissueGnostics hardware platforms including TissueFAXS Plus, TissueFAXS SL (supporting up to 120-slide batch runs), TissueFAXS Spectra and Spectra SL for multispectral fluorescence imaging, and TissueFAXS Q, iQ, and SLQ for high-speed spinning disk confocal imaging. Support is provided by a multidisciplinary team covering hardware configuration, image analysis, system maintenance, and biology, with application specialists and R&D teams available for custom workflow development.