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 workflow based on Metafer 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 ultra-flexible imaging workflow 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 triggers from outside (e.g., from a LIMS or a bar code).

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


Metafer MetaCyte 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 provide proposals for 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 pre-select cells they can easily interpret, while tending to ignore the difficult-to-interpret cells. The automated scanning solution 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, people spend significant time to correct automated results, or to reject cells they do not like. With Metafer this can be different: MetaSystems created RapidScore, a new method of analyzing FISH signals which combines manual scoring strategies with the advantages of automated scoring. RapidScore uses Metafer MetaCyte 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 any time. An empty scoring sheet displayed 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.

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Tissue FISH

Metafer 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 Metafer TissueFISH.

First of all, 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. On 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 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.

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Order Information

Metafer BASE


The basis module Metafer BASE is a software for opening and reviewing Metafer data files, displaying measurement results, and manual confirmation of data.

Metafer SCAN


The Metafer SCAN module provides scanning functionality and serves as a basis for complete automated scanning systems. This includes the support of suitable scanning hardware (such as microscope, motorized stage, camera), the implementation of intelligent auto-focus algorithms, coordinate management, relocation function, and more. Includes Metafer BASE.

Metafer IMAS


The basis module Metafer IMAS is a software for manual image acquisition of images. Includes Metafer BASE.

Metafer MetaCyte


The analysis module Metafer MetaCyte extends a Metafer basis module with the functionality of multi-parametric object analysis. Requires a Metafer basis module.

The list above is not exhaustive, and technical data may change. Please contact your MetaSystems representative for further explanations and details.


Legal Note

MetaSystems software and system products are classified as in vitro diagnostic medical devices (IVD) in the European Union in accordance with In Vitro Diagnostics Regulation (EU) 2017/746 or In Vitro Diagnostic Medical Device Directive 98/79/EC, respectively, and carry the CE label unless otherwise indicated. Use all MetaSystems IVD products only within the scope of their intended purpose.

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 diagnostics.

Some hardware components supplied by other manufacturers are not included in MetaSystems IVD products and are therefore not IVD medical devices.

Please contact us for further information.