Signal Analysis

RapidScore: Automation of FISH Spot Counting

Unattended and automated analysis of fluorescence signals, signal fusions, and spot patterns.

The analysis of fluorescence signal patterns / FISH spots in cells or cell nuclei is the basis for many assays in hematology and cancer genetics. With the automated fluorescence signal analysis system, based on the Metafer platform (MetaCyte), these patterns are analyzed automatically, precisely, and reproducibly. Results are stored together with the cell or nuclei images, and they can be displayed in the image gallery, in histograms and scatter plots, or as a summary table in one of Neon's beautiful reports.

The system's ultra-flexible architecture allows for addressing principally any imaging task. Signal channels can be combined to an assay, and the images obtained in each channel can be processed individually. Morphology of target cells, nuclei, or other objects can be precisely defined with a number of cell selection parameters. More than 300 features of objects (e.g., of area, shape, intensity, and signal distribution) can be measured. The results of such a measurement can recursively be used to trigger other features, so that extremely sophisticated analyses can be done for each single image. All the parameters are then stored within a classifier, setting the scoring standard for many future experiments. Once created, a classifier can be selected with some simple mouse clicks, or even by external triggers (e.g., from a LIMS or a bar code).

The powerful tools of Metafer assist in providing image analysis solutions in many fields of work. Toxicologists, microbiologists, pathologists, hematologists, and many other researchers and laboratory professionals worldwide rely on the outstanding characteristics of the system.


Metafer1 does a lot more than simply counting signals: for example, it is also able to identify and count fusions of signals from different color channels. In this way, the software has the capability to analyze all signal patterns found in samples hybridized with MetaSystems Probes' locus-specific probes. If it comes to automation of signal analysis, it often appears that human scorers preselect cells they can easily interpret, while tending to ignore the difficult-to-interpret cells. The automated scanning system provides unbiased interpretation, scoring many cells that are often ignored via manual spot counting. Therefore, many labs are used to working with very low abnormal cut off values for positivity during manual observation. As a result of these discrepancies between automated and manual scoring strategies, technologists spend significant time to correct automated results, or to reject cells they do not like. With Metafer1, this can be different: MetaSystems created RapidScore (RS), a new method of analyzing FISH signals which combines manual scoring strategies with the advantages of automated scoring. RS uses Metafer1 to automatically score cell signal patterns. All analyzed cells are displayed in a gallery. Signal patterns are summarized in a convenient graph and a table. Immediately after, the scan technicians can begin categorizing cells with doubtful results. Categories are assigned to each cell using an external keypad, and new categories (groups of cells) can be added at any time. An empty scoring sheet, which is visible to the left of the automated results, dynamically displays the manual results while the categorization is proceeding. An enlarged image of the unprocessed cell in question facilitates evaluation of signal patterns.

Need Help?

Tissue FISH

Metafer1 is very strong in the analysis of FISH patterns in single cell nuclei, but it can do a lot more than this. Fluorescence signals in tissue sections, for instance, can be easily analyzed with the dedicated software interface of Metafer1.

Firstly, multiple options for pre-scans can be used to provide sample overviews. Pre-scans could even be done on a separate sample with a subsequent H&E stained tissue section. Regions of interest can be marked in the tissue viewing software, and a convenient tool to edit tissue micro array (TMA) patterns facilitates high-throughput analyses.

Once images of selected regions in the tissue, or the TMA, are acquired automatically, they can be loaded into the dedicated user interface. Cells of interest are quickly selected with pen or mouse. Upon selection, all FISH signals in the selected cell/nucleus are automatically analyzed. Analysis can encompass counting of signals, but also the detection of fused signals, a quantification of intensities, the identification of split signals, and much more. Results for each nucleus are shown together with a gallery image, thus offering the possibility to immediately check and correct the data. The configurable data histogram is updated with each nucleus that is added to the gallery. After finishing the analysis, data can be summarized and printed.

Though nucleus selection is done very conveniently in the software interface, special algorithms are available for automated nucleus segmentation. Pre-segmented nuclei can quickly be included in the analysis using a pen tip or a mouse click. A toolkit of dedicated image processing operations offers image enhancement prior to analysis. It is possible to quickly switch between the original and the processed image. Due to this functionality, Metafer1 has been successfully applied to assess solid tumors, regardless of whether based on conventional tissue sections or on TMA preparation.

Need Help?
1 MetaSystems products are used in many countries worldwide. Depending on the regulations of the respective country or region, some products may not be used for clinical diagnostic use. In Europe MetaSystems products are CE labelled in-vitro diagnostics (IVD) devices. In the USA all MetaSystems products except the Ikaros karyotyping systems are intended to be used for research or inspection only.