TissueFISH
Applying Spot Counting to Tissue Sections
The following customizations were most favored by our clients:
- Various pre-scan options are available for creating sample overviews.
- Tissue matching capabilities, such as alignment with a separately H&E-stained tissue section.
- User-friendly tools for dissecting Tissue Microarray (TMA) patterns.
- Automated image acquisition for specific regions within tissue sections or TMAs.
- Integration of advanced Deep Neural Network (DNN)-based methods for automatic nucleus segmentation.
- Efficient selection of cells of interest using a pen or mouse.
- Automated suggestions for signal patterns.
- A customizable data histogram that updates dynamically with each object added.
The Tissue FISH customization within the Metafer Platform Software integrates advanced software with cutting-edge imaging techniques, suggesting a powerful workflow for analyzing FISH signals in tissue sections. Users can select from various pre-scan options to generate overviews of their tissue samples. This includes the ability to perform pre-scans on a separate H&E (Hematoxylin and Eosin) stained sample to identify regions of interest. These marked regions can then be transferred to the analysis sample, allowing for tissue matching to target the corresponding areas in adjacent tissue sections. For high-throughput analyses, the software includes a convenient tool for editing Tissue Micro Array (TMA) patterns.
Once the regions of interest are identified, the software can automatically capture images of the selected areas. The intuitive interface allows users to quickly choose cells of interest using a pen, or mouse, or through a custom workflow that incorporates automated segmentation with user-trained Deep Neural Networks (DNN). Pre-segmented nuclei can be easily added to the analysis with a simple pen tip or mouse click. Once selected, the software automatically generates proposals indicating potential signals, which can be displayed alongside a gallery image for real-time verification and correction. Additionally, a configurable data histogram updates dynamically as each object is added to the gallery, providing a clear visual summary of the data during the review process. The Metafer Platform Software also includes a comprehensive set of image processing tools, enabling significant enhancement of images before analysis. Users can effortlessly toggle between the original and processed images for comparison.
The Customization Package TissueFISH is a service to set up a proposed workflow that utilizes the various tools of the Metafer Platform Software to provide a comprehensive solution for analyzing fluorescence signals in tissue sections. It integrates advanced software with automated image acquisition and processing tools, simplifying the analysis of FISH spots and other fluorescence signals in tissue samples. Our TissueFISH Customization Package offers a service to assist customers in designing, implementing, and validating their workflows, with support from a MetaSystems application specialist. Final workflow validation is the responsibility of the customer.
Each tissue sample is unique, making it ineffective to configure scanning software like Metafer to always digitize the same region. Instead, Metafer provides flexible options for creating intelligent autofocus algorithms that adapt to the dimensions and characteristics of tissue sections on the specimen. To prepare for the main scan, a pre-scan at the lowest possible magnification can be configured and conducted before the main scan. This pre-scan automatically generates an optimized position list for the main scan, allowing users to define criteria for selecting optimal regions, such as cell density, signal presence, tissue thickness, and more. Additionally, through a tissue-matching process, pre-scans can be applied to differently stained adjacent sections. Regions captured automatically or marked manually can then be transferred to another tissue section for further analysis.
In an ideal, customized TissueFISH workflow, results for each nucleus are displayed alongside a gallery image, enabling immediate verification and correction. The software dynamically updates a configurable data histogram to summarize the findings in real-time. For final review, it provides a comprehensive overview, including the cell gallery, a virtual DAPI slide, and the corresponding H&E virtual slide. Results can be exported either as raw data or in customizable report formats.
- Metafer (5.0MB)
Metafer, MetaSystems' scanning and imaging software, controls microscope and accessory hardware to acquire digital images, and to assist the operator in the detection, classification, and counting of cells of human or other origin and other objects in microscopic specimen.
- Case and Image Data Management (1.3MB)
Neon is a technology for the flexible and consistent management of image and case data. It is designed to collect data from a variety of sources and integrate them into an efficient and well-structured workflow. The technology integrated in all MetaSystems installations ensures that all relevant information is available wherever it is needed.
MetaSystems software provides, among other functions, features to assist users with image processing. These include, but are not limited to, the use of machine and deep learning algorithms for pattern recognition. The output generated in this process should be regarded as preliminary suggestions and, in any case, mandatorily requires review and assessment by trained experts.
MetaSystems offers Customization Packages for application workflows that have been successfully implemented for customer labs using standard Metafer platform functionality. It is expected that they can be implemented for other customer labs using similar workflows and slide preparation procedures. If a Customization Package is purchased, MetaSystems product specialists will – based on their experience from other similar application cases - support the customer lab in adapting the Metafer software configuration to their needs. The performance of the solution will depend on the quality of the customer slides and the expertise of the users, MetaSystems cannot specify or guarantee any performance parameters. The validation of the solution for clinical use is the sole responsibility of the customer lab.