Automatic Analysis of Fluorescence-based Assays: CaeT2

Our Motivation – Efficiency and Reproducibility

Research and development in life sciences like pharmacology, microbiology, virology and immunology demand fluorescence-based analysis of cells under the microscope. Therefore, various fluorescence stains are applied to image the different cell structures (cytoplasm, cell nucleus etc.).

The analysis and interpretation of such data sets, most of them very large with hundreds of images still is a time- and labor-intensive manual process. Insufficient reproducibility by subjective assessment and an evaluation depending on the form of the day can influence the interpretation and restrain the significance of results.

High data quality and reproducibility as well as efficient and economic analysis will also decide about success in research. At this point the Fraunhofer IIS supports you with productive and customized software solutions for computer-assisted fluorescence evaluation. 

Our solution – Fast and Automated

Software “CaeT2“
© Fraunhofer IIS
"CaeT2" can display fluorescence images of various Fluorescent dyes, e.g. DAPI, Hoechst, cyanine. Typical applications are, i.a. cell counts, transfection and cell viability.
Review of free software tools for image analysis of fluorescence cell micrographs
© Fraunhofer IIS
Referring to: Wiesmann, V.; Franz, D.; Held, C.; Münzenmayer, C.; Palmisano, R.; Wittenberg, T.: Review of free software tools for image analysis of fluorescence cell micrographs.

Our analysis technology “CaeT2“ (“Cell analysis and evaluation Tool 2“) is able to adapt automatically to new analysis tasks. Therefore, the user can train the system with just a few example images by manual annotation with the mouse or alternative input devices to new cells or modalities. A mathematical optimization procedure determines the ideal parameter settings automatically. That is why no complex manual parameter settings or expert knowledge for image processing is necessary for using “CaeT2“. “CaeT2“ can process fluorescence images of different fluorescence stains like DAPI, Hoechst, cyanine and others. Typical applications are e.g. cell counting, transfection and cell viability assays.


The software “CaeT2“ offers the following features:

  • Detection and segmentation of cells in fluorescence images
  • Automatic cell counting and statistics
  • Calculation of parameters


We are steadily improving our analysis platform with these advantages for you:

  • Objective and timesaving analysis
  • Easy and intuitive user interface
  • No skills of image analysis or programming necessary
  • Automatic parameter configuration by example images
  • Pre-configured process pipelines
  • Optional add-on to the software of a big manufacturer of microscopes


A lot of free tools offer a high functionality but are hard to operate and require long training periods. “CaeT2“ closes this gap as an easy-to-use software for biologists and other professions without image processing and programming knowledge.

Our Offer

We would like to consult you to the applications and options for use of the software “CaeT2“. It is also possible to use and license “CaeT2“ as a software library.  Fraunhofer IIS would be glad to support you in the adaption and integration into existing solutions. Please contact us for further information.

Please note: It is only allowed to use the software “CaeT2“ for research purposes. It is not allowed to use “CaeT2“ for medical diagnosis.





  • Wiesmann, V.; Bergler, M.; Palmisano, R.; Prinzen, M.; Franz, D.; Wittenberg, T.; Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms, In: BMC Bioinformatics, (2017), 18:176, doi: 10.1186/s12859-017-1591-2.
  • Wiesmann, V.; Franz, D.; Held, C.; Münzenmayer, C.; Palmisano, R.; Wittenberg, T.: Review of free software tools for image analysis of fluorescence cell micrographs, doi:10/1111jmi.12184.

More Information


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Software based Image Analysis and Enhancement

Our focus are the domains of Microscopy and Endoscopy.