• Leverage multiple pre-scan options to generate comprehensive sample overviews, including the ability to perform pre-scans on a separate H&E stained tissue section.
• Mark regions of interest within the tissue viewing software and utilize a convenient tool for editing Tissue Microarray (TMA) patterns, facilitating high-throughput analyses.
• Automatically acquire images of selected regions in the tissue or TMA, which can then be loaded into the dedicated user interface for further analysis.
• Select cells of interest quickly using a pen or mouse, with automatic analysis of all FISH signals within the selected cell/nucleus, including signal counting and intensity quantification.
• View results for each nucleus alongside a gallery image, allowing immediate verification and correction. A configurable data histogram updates with each added nucleus.
• Utilize special algorithms for automated nucleus segmentation, easily incorporating pre-segmented nuclei into the analysis with a pen tip or mouse click.
• Access a comprehensive toolkit of image processing operations to enhance images prior to analysis, with the ability to switch quickly between the original and processed images.
• Manage cases and images efficiently with Neon, our sophisticated image management tool, designed to streamline your workflow and enhance data organization.

Metafer TissueFISH combines sophisticated software with advanced imaging techniques to provide a robust platform for analyzing fluorescence signals in tissue sections. Whether through manual selection or automated segmentation, the system offers features to enable a precise and efficient analysis, making it an invaluable tool for high-throughput tissue studies.

Metafer is a highly sophisticated platform renowned for its robust capabilities in the analysis of FISH (Fluorescence In Situ Hybridization) patterns within single cell nuclei. However, its versatility extends well beyond this primary function. Specifically, Metafer TissueFISH is designed for the comprehensive analysis of fluorescence signals in tissue sections, equipped with a specialized software interface that makes this complex process both efficient and user-friendly.

One of the standout features of Metafer TissueFISH is its flexibility in pre-scan options. Users can choose from multiple pre-scan methods to create detailed overviews of their samples. This includes the innovative option to perform pre-scans on a separate sample that has been H&E (Hematoxylin and Eosin) stained, providing a reliable reference that enhances the accuracy and ease of subsequent analyses.

The system's tissue viewing software is designed to be intuitive and efficient. Users can easily mark regions of interest within the tissue, ensuring that analysis is focused and relevant. For high-throughput analyses, the software includes a convenient tool for editing Tissue Micro Array (TMA) patterns, streamlining the workflow and significantly saving time.

Once the regions of interest have been identified, Metafer TissueFISH automates the image acquisition process. Images of the selected regions are captured and then seamlessly loaded into the dedicated user interface. Here, users can quickly select cells of interest using either a pen or mouse. Upon selection, the software automatically analyzes all FISH signals within the selected cell or nucleus. This analysis is comprehensive, encompassing signal counting, fused signal detection, intensity quantification, and the identification of split signals, among other parameters.

The system is designed to provide immediate feedback and validation. Results for each nucleus are displayed alongside a gallery image, allowing users to verify and correct the data in real-time. Additionally, a configurable data histogram updates dynamically with each nucleus added to the gallery, providing a clear visual representation of the data as the analysis progresses.

For those who require even more efficiency, Metafer TissueFISH offers automated nucleus segmentation through advanced algorithms. Pre-segmented nuclei can be easily incorporated into the analysis with just a pen tip or mouse click, further accelerating the process.

Image quality is paramount in any form of fluorescence analysis, and Metafer TissueFISH does not disappoint. The platform includes a comprehensive toolkit of dedicated image processing operations that allow for significant enhancement of images prior to analysis. Users can quickly switch between the original and processed images, ensuring that the best possible data is used for analysis.

In summary, Metafer TissueFISH is a powerful and versatile tool that brings a new level of efficiency and accuracy to the analysis of fluorescence signals in tissue sections. Its combination of advanced automation, user-friendly interface, and comprehensive processing capabilities makes it an invaluable asset for any laboratory engaged in high-throughput tissue studies.

MetaSystems has designed a smart scanning workflow of hybridization and imaging tools to be integrated in the routine workflow of the pathology lab. Core of this solution is the combination of dedicated DNA probes for tissue sections with the innovative scanning facilitated by the Metafer software, merged to a flexible and robust slide scanning with many options.
The integrated scanning system managed by the Metafer SCAN software automatically generates virtual slides in brightfield and fluorescence, acquires high resolution FISH images and provides an automatic score. Equipped with an automated bar code reader and the robust SlideFeeder x80 for up to 800 samples, it can be operated in a 24/7 mode.

1. As initial step a digital brightfield, e.g., H&E slide is generated. The pathologist calls up the digital slide and selects on screen the tumor region on the virtual slide that needs to be FISH-scored.

2. Next, the FISH slide (from a subsequent section of the same block) is being scanned at low magnification to generate an overview. Displayed side by side to the marked digital H&E image the tumor region can easily be transferred to the FISH slide.

3. The Metafer SCAN software now has all the information to start automatic image acquisition of the FISH slide at higher magnification. Cell nuclei that are isolated or slightly connected will be separated automatically and spot-counted. Manual tools for segmentation help to separate touching nuclei for immediate automatic scoring until the preset number of cells to be analyzed has been reached. The software module can be easily set up to match the individual analysis standards. For instance, it is possible to define a minimum number of cells to be analyzed, and also to define a number of independent readers.
   More on signal analysis in tissue sections can be seen here.

4. For final review the software presents a full synopsis to the pathologist, comprising the cell gallery with the scoring results, the virtual DAPI slide showing the positions of analyzed cells, and the corresponding H&E virtual slide. Every cell can be traced back to the tissue section to confirm its location within the preselected tumor region.

5. Final results can either be exported as raw data, e.g., for subsequently being processed by external software, or can be summarized in comprehensive, user-adaptable reports.

The laborious nature of procedures, shortages of sample material, and limitations in the cost of reagents for diagnostics in routine clinical pathology has raised the interest in high throughput solutions. The tissue micro-array (TMA) technique addresses these issues by obtaining small tissue cores from regions of interest in paraffin embedded tissues, assembling them in an array-like fashion, and mounting them to a standard glass slide for microscopy. Each of these cores then represents an independent analysis case.

Due to the special layout of samples automation of TMA has to be done based on the following considerations:

• Analysis should take the general layout of the TMA into account,
• It should be possible to correct contortions, rotations, or other spatial aberrations generated during slide preparation,
• Each TMA core should be clearly identifiable by a label,
• Analysis results should be separable so that data can be assigned to the single core.

With the unique combination of scanning capabilities facilitated by the Metafer software, the integrated tool for TMA analysis, and the sample digitization software, MetaSystems offers a complete package for precise and effortless automated TMA analyses. Once a tissue microarray (TMA) is created, its layout can be expressed with the number of cores per row, the number of rows in the array, the diameter of the cores, and the distance of cores. In the integrated Metafer TMA tool these values can be used to generate a TMA map file that is used as basis for the analysis. Additionally, each core can receive a unique identifier.

A fast pre-scan at low magnification is used to generate a map of the current slide. The result of the pre-scan is displayed side by side with the TMA map, and with a flexible grid the actual image can be matched to the map in order to correct any spatial aberrations. Missing or invalid cores can be marked in this interface. On confirmation the TMA tool converts the data into a position list, which contains the exact positions of each core, and also the core identifiers. The scanning workflow is now ready to re-locate each core and acquire and analyze the core images. If the image stitching software is available, core images are automatically composed in the background and an overview image of the whole TMA is generated.

What is Metafer TissueFISH?
Metafer TissueFISH is an advanced platform designed for comprehensive analysis of fluorescence signals in tissue sections. It combines sophisticated software with automated image acquisition and processing tools to streamline the analysis of FISH patterns and other fluorescence signals in tissue samples.

What types of samples can Metafer TissueFISH analyze?
Metafer TissueFISH can analyze a variety of tissue sections, including those stained with FISH probes. It is also compatible with pre-scanned H&E stained sections, allowing for detailed comparison and analysis.

How does the pre-scan process work?
The pre-scan process involves creating an overview of the sample using multiple scanning options. This can include a separate pre-scan of an H&E stained tissue section, which serves as a reference for identifying regions of interest on the FISH slide.

Can Metafer TissueFISH operate continuously?
Yes, the system is equipped with an automated bar code reader and the SlideFeeder x80, which can handle up to 800 samples. This allows for continuous operation in a 24/7 mode, ensuring high throughput and efficiency.

How are regions of interest identified and transferred?
Initially, a digital brightfield slide (e.g., H&E) is created, and the pathologist selects the tumor region on the virtual slide. This region is then transferred to the corresponding FISH slide, which is scanned at low magnification to generate an overview, facilitating precise region identification.

What types of analyses can be performed on FISH signals in tissue?
Metafer TissueFISH allows for comprehensive analysis, including counting of signals, detection of fused signals, quantification of intensities, and identification of split signals. The software supports both automatic and manual segmentation and scoring of cell nuclei.

How are results verified and reported?
Results for each nucleus are displayed alongside a gallery image for immediate verification and correction. The software dynamically updates a configurable data histogram. For final review, it presents a full synopsis, including the cell gallery, virtual DAPI slide, and corresponding H&E virtual slide. Results can be exported as raw data or summarized in customizable reports.

How does Metafer TissueFISH enhance image quality?
The platform includes a comprehensive toolkit for image processing, allowing for significant enhancement of images before analysis. Users can switch between the original and processed images to ensure the best possible data quality.