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The Cell-Shape-Wizard

User Guidance for Active Contour-Based Cell Segmentation
  • Daniela Franz
  • H. Huettmayer
  • Marc Stamminger
  • Veit Wiesmann
  • Thomas Wittenberg
Conference paper
Part of the Informatik aktuell book series (INFORMAT)

Abstract

Cell segmentation on fluorescent micrographs requires preprocessing, cell-background separation and cell-cell separation. The presence of touching or overlapping cells requires more sophisticated segmentation methods – such as Active Contours (AC) – for cell-cell separation, but the usage and parametrization of these methods is often infeasible for users with no image processing expertise. We present the Cell-Shape- Wizard which introduces an abstraction layer between a complex AC approach and the users. It couples tight user guidance with the benefits of interactive cell segmentation of fluorescence micrographs. We have evaluated the wizard in a small user study with four subjects. Results show, that the wizard concept is well applicable to cell segmentation. Segmentation results are compared to manual reference annotations and result in a mean Jaccard index of 0.72. With the Cell-Shape-Wizard life scientist are able to segment their fluorescence micrographs semiautomatically on their own, without being forced to acquire additional knowledge in image processing.

Keywords

Active Contour Jaccard Index Abstraction Layer Active Shape Model Segmentation Task 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Zhao T, Murphy RF. Automated learning of generative models for subcellular location: building blocks for systems biology. Cytometry A. 2007;71:978–90.CrossRefGoogle Scholar
  2. 2.
    Wiesmann V, Franz D, Held C, et al. Review of free software tools for image analysis of fluorescence cell micrographs. J Microsc. 2014; p. online.Google Scholar
  3. 3.
    Franz D, Wiesmann V, Stamminger M, et al. Cell-shape wizard: a concept for userguidance for active shape segmentation in fluorescence cell micrographs. Biomed Tech. 2014;59(s1):77–80.Google Scholar
  4. 4.
    Tidwell J. Designing Interfaces. O’Reilly; 2007.Google Scholar
  5. 5.
    Carpenter AE, Jones TR, LamprechtMR, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2007; p. 7:R100.Google Scholar
  6. 6.
    M¨oller B, Posch S. A framework unifying the development of image analysis algorithms and associated user interfaces. Proc MVA. 2013; p. 447–50.Google Scholar
  7. 7.
    Kass M, Witkin A, Terzopoulus D. Snakes: active contour models. Int J of Comput Vis. 1988; p. 321–31.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Daniela Franz
    • 1
    • 2
  • H. Huettmayer
    • 1
  • Marc Stamminger
    • 2
  • Veit Wiesmann
    • 1
  • Thomas Wittenberg
    • 1
  1. 1.Fraunhofer Institute for Integrated Circuits (IIS)ErlangenDeutschland
  2. 2.Computer Graphics GroupUniversity of Erlangen-NurembergErlangen-NurembergDeutschland

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