The Metafer software conveniently automates a wide area of image analysis applications in microscopy for life sciences.

Due to Metafer's modularity and its flexible architecture, it is applicable to a large variety of applications. Around 1,500 Metafer managed scanning platforms are worldwide in use for metaphase finding, processing of FISH signals and toxicological assays, digitization of samples, and much more.



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Metafer managed imaging systems scan specimen of various sizes, use many different contrasting methods and magnifications, and find many different target objects. Due to Metafer's modularity and its flexible architecture, it is applicable to numerous applications, including cytogenetic diagnostics, hematology, pathology, toxicology, forensic sciences, and many more.

Of course, automated imaging saves time. But even more important is reproducibility, achieved by applying clearly defined standards to any analysis - slide by slide, experiment by experiment, and patient by patient. This way, smart scanning managed by the Metafer software adds an unbiased degree of quality to your results. Complex analysis systems tend to be cumbersome and difficult to understand. Smart scanning managed by the Metafer software is much different: unlimited access to all data, convenient display of results, and full control of all evaluation parameters guarantee that results are generated exactly the way you want. Slide scanning becomes extremely easy with Metafer.

Each microscopic sample is different: automation of analysis therefore demands flexibility. Metafer’s unique concept provides a powerful solution: user-trainable classifiers precisely define the analysis standards, and with the selection of the appropriate classifier the integrated scanning system is quickly switched to the next assay.

Solutions by MetaSystems grow with demand. Software and integrated hardware are modular, and with higher workloads the level of automation can be increased; optional features such as the SlideFeeder x80, the automated Bar Code Reader, and the automated Immersion Oil Dispenser are easily added upon demand.

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As part of Ikaros and Metafer, Neon is the convenient interface for organizing case and image data. Users configure overview dashboards to summarize cases, processing statuses, and case statistics. Interfaces for data exchange with external databases can be adapted. The fields on case data sheets and reports are customizable to meet specific needs.

Read more about Neon.

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Smart scanning based on the Metafer software is highly flexible with many options, and every application has certain hardware and software requirements. A number of different software modules and hardware options are available. Please contact MetaSystems to receive a detailed recommended system configuration for your applications.

In general, integrated systems managed by the Metafer software come with 1 of 4 different camera models and with a motorized stage. A full system integration requires a motorized microscope. MetaSystems is able to also integrate the microscope with the system, but the Metafer software can also integrate with existing, compatible microscopes.

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 RELO


The basis module Metafer RELO is used to relocate objects according to their coordinates on the slide. Includes Metafer BASE.

Metafer IMAS


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

Metafer Metaphase


The analysis module Metafer Metaphase extends a Metafer base module with the functionality of metaphase finding and metaphase image acquisition. Requires a Metafer basis module.

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.

Metafer RCDetect


The analysis module RCDetect is software for the detection of rare cells based on specific staining patterns. It uses a special algorithm that combines highest speeds with detection precision. Requires a Metafer basis module.

Metafer CometScan


Metafer CometScan is an application package for the automated evaluation of cells prepared with the Single Cell Gel Electrophoresis (Comet) assay. The software evaluates the cells based on the intensities and automatically calculates parameters such as the Tail Moment, the Tail Moment (Olive), the lengths of head and tail, and many more. Requires a Metafer basis module.

Metafer DCScore


The application package Metafer DCScore finds dicentric chromosomes in images of metaphases, counts them and displays them in the image. The software processes both Giemsa-stained chromosomes and those stained with PNA probes for telomere and centromere regions. Requires the analysis module Metafer Metaphase.

Metafer MNScoreX


The application package Metafer MNScoreX finds binucleated cells prepared for the cytokinesis block micronucleus assay and quantifies the micronuclei in these cells. All evaluated cells are displayed in an image gallery and the number of micronuclei is shown in the image corners. Requires a Metafer basis module.

Metafer TissueFISH


The application package Metafer TissueFISH extends Metafer with functions that are especially useful for the evaluation of FISH signals in tissue sections. Metafer TissueFISH offers the user an optimized environment in which cells in the tissue can be segmented, selected, and evaluated. The results of the evaluation are immediately visible in a small cell gallery. Requires the analysis module Metafer MetaCyte.

Metafer SpermFinder DNN


The application package Metafer SpermFinder DNN uses artificial intelligence (so-called Deep Neural Networks; DNN) to enable a scanning system for the detection of sperm cells in forensic specimens. The module supports specimens stained with the so-called ‘Christmas Tree’ staining (Nuclear Fast Red/PIC), as well as the Baecchi staining (Acid Fuchsin and Methylene Blue). Requires a Metafer basis module.

Metafer DNN


Metafer DNN is a technical module that enables Metafer to run image analysis algorithms using artificial intelligence (Deep Neural Networks; DNN). Requires a Metafer basis module.

Metafer DNN Server


Installed on a suitable workstation in the network, the technical module Metafer DNN Server takes analysis tasks from other Metafer instances and performs the image analysis.

Metafer VSlide


The technical module Metafer VSlide is a software that stitches single images acquired by Metafer SCAN into larger images. For this purpose, the software uses special algorithms and allows fine adjustment of the stitching parameters. Requires a Metafer basis module.

Metafer BarCode


The technical module Metafer BarCode enables Metafer software to read and interpret bar codes on slides and slide frames. It requires a compatible bar code reader or a microscope that is capable to read bar codes with the objective. Requires a Metafer basis module.

Metafer Remote Analysis


The technical module Metafer Remote Analysis is software that can pass image analysis tasks for Metafer generated data to a Metafer instance installed on another workstation. In this way, the Metafer SCAN installation can be relieved of time-consuming calculations. Requires Metafer SCAN or Metafer IMAS for generating the images and a Metafer BASE installation with suitable analysis module.

Metafer HighRes


The Metafer HighRes technical module enables the support of high-resolution cameras (12 MP) on Metafer-powered devices.

HL7 Interface for Ikaros / Metafer


This technical module for Ikaros and Metafer enables the exchange of images and data based on the Health Level 7 (HL7) standard.

DICOM Interface for Ikaros / Metafer


This technical module for Ikaros and Metafer enables the exchange of images and data based on the standard for Digital Imaging and Communications in Medicine (DICOM).

GLP Upgrade for Ikaros / Metafer


The GLP Technical Module adds features to Ikaros or Metafer installations that make the software compatible with Good Laboratory Practice (GLP) regulations.

Metafer VSViewer


In the viewer module Metafer VSViewer, composite microscope images as generated by Metafer VSlide can be displayed. Metafer VSViewer offers a large number of different tools for this purpose, which allow easy navigation in the image, virtual focusing, annotating features in the image, as well as displaying color separations and images with modified colors.

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


The current CE labeled software version is Metafer 4.3. The information about Metafer in our online presence refers to this version number.

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.

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For special applications, a variety of software upgrades are available. Software upgrades require a functional Metafer system and a defined main module, which provides the basic tools required for the scan.