StrataQuest

StrataQuest, developed by TissueGnostics, is an image analysis platform designed for phenotyping, quantification, and spatial analysis of both brightfield and fluorescence tissue images. It functions as a contextual tissue cytometer, supporting workflows that range from simple image filtering to advanced multiplexed analysis, AI-based segmentation, and data mining. The platform is suited to researchers across a broad range of biomedical disciplines, including oncology, immunology, neurology, dermatology, and osteology, as well as core facilities and labs requiring standardized or outsourced analysis.

StrataQuest supports custom workflow creation, batch analysis, and real-time preview, and is available in multiple configurations depending on user needs and technical expertise. Version 8.0 introduces redesigned interface elements, expanded data mining tools, and integrated dimensionality reduction methods.

Core Features

• Phenotyping and Phenotype Interactions: Define cellular subpopulations using Boolean logic (e.g., CD3+CD8+PD1–). Phenotypes can be displayed on images and in diagrams. The phenotype interaction tool assesses spatial relationships between phenotypes by allowing users to define a maximum distance in micrometres and analysing potential interactions within that range.
• Dot Detection: Analyses staining patterns within individual cells, including dot-based techniques such as FISH and CISH. Supports visualisation of dots per cell and co-expression analysis across multiple colour channels.
• AI Nuclei Segmentation: Offers both classical and deep learning-based approaches to nuclei segmentation. The deep learning method is designed for challenging tissues, including those with weakly stained or densely packed nuclei.
• Machine Learning-Based Tissue Classification: Users train a classification engine by drawing lines on tissue areas. The classifier distinguishes macrostructures such as crypts, stroma, and background, enabling differentiation of histological regions.
• Proximity Measurement: Analyses distribution patterns of phenotypes within defined distances from tissue structures such as tumour islets. Outputs include graphical distance maps with customisable ranges and backward links to original images for cross-referencing.
• Unlimited Multiplexing: Supports analysis of low-plex and high-plex datasets with no fixed limit on the number of markers per sample. Integrated data mining tools assist in interpreting complex high-plex data.
• Custom Statistics and Batch Analysis: Statistical output can be tailored to specific experimental requirements. Workflows can be saved and automated for consistent batch processing without manual adjustments.
• Versatile Data Export: Exports cell and tissue measurement data, overlays, images, image masks, and diagrams in formats including JPG, TIFF, BMP, and PNG. Statistical reports and data tables can be exported to Excel or CSV formats.
• Interactive Diagrams: All plots are forward- and backward-connected, allowing users to track individual cells across diagrams and back to their spatial location in the tissue.
• Real-Time Analysis Preview: Parameter adjustments are reflected immediately in a 512×512-pixel preview, reducing trial and error and speeding up workflow configuration.
• Prebuilt Pipeline Library: Provides access to over 70 ready-to-use analysis pipelines (Apps) covering applications in osteology, neurology, oncology, immunology, dermatology, and more. Custom pipeline development is also available.

New and Updated in StrataQuest 8.0

• Advanced Data Mining Tools: Includes t-SNE, UMAP, and SONG for dimensionality reduction, accessible with a single click. Violin plots support comparison of marker expression across multiple phenotypes. 3D diagrams allow exploration of three phenotypes along x, y, and z axes.
• Redesigned User Interface: Features an improved Layer Editor, an Image and Category Toolbar for verification, an Object Inspector with clearer raw data access, a customisable workspace with draggable panels, a new Project Database view with thumbnails and slide previews, and integrated Bio-Formats import for broader file compatibility.
• Expanded Interactive Diagrams: Version 8.0 adds integrated t-SNE, UMAP, SONG, and Violin Plot tools directly within the software environment.

Upcoming Features (Version 8.1)

• AI Center: A platform for training, managing, and storing deep learning and machine learning models within StrataQuest. Users will be able to fine-tune AI models using their own annotated data without switching between external tools.
• Omics Explorer: Supports import and analysis of multi-omics data from platforms including MERFISH (Vizgen), 10x Genomics, and NanoString. Enables correlation of spatial gene expression, protein data, and morphological features by linking omics results with image data and StrataQuest analysis outputs.

Available Configurations

• StrataQuest Plus: Targeted at researchers with multiple projects and core facilities. Supports creation of unlimited pipelines and Apps. Available under perpetual or annual licensing with maximum workflow flexibility.
• StrataQuest App Platform: Designed for labs using standard protocols and technical staff. Provides a simplified interface with fixed diagrams and data export. Apps are purchased individually or in packages under a perpetual licence; pricing depends on complexity.
• StrataQuest Analysis Service: An outsourced option for labs requiring small-batch image analysis. TissueGnostics performs the analysis and delivers results; scanning can be included. Pricing is based on sample complexity and volume. Completed workflows can be purchased as Apps.

Example Apps in the App Center

• IF Artificial Skin: Stratifies skin equivalents into dermis and epidermis, segments the stratum corneum and additional layers, and quantifies staining intensity, area, nuclei, and marker-positive cells per layer.
• IF Cardio Cell Culture Dots: Segments cultured cardiac cells, detects cardiomyocytes and fibroblasts, and quantifies dot markers (CISH/FISH) per cell including dot count, area, and mean intensity.
• IF Brain App: Classifies brain regions using an AI-based classifier, detects cellular phenotypes such as astrocytes, and quantifies tissue areas and phenotype counts across regions.
• IF 4: Analyses single-cell co-expression of four fluorescence markers, segments cells into nucleus, perinuclear area, and/or cytoplasm, and exports up to 20 intensity, statistical, and morphometric parameters.
• IHC Adipocytes+: Detects adipocytes and cellular aggregates, with outputs including number and area measurements.
• IHC Lung Cancer Mouse: Segments murine lung sections into tumour and non-cancerous tissue using a machine learning classifier, detects hematoxylin-stained nuclei, and quantifies tumour area and marker-positive phenotypes.

StrataQuest integrates with TissueFAXS scanning systems and supports Bio-Formats file import for compatibility with a wide range of imaging sources. Custom App development is available through consultation with TissueGnostics application experts. The platform is supported by a knowledge base of white papers, application notes, and webinars covering use cases across multiple research domains.