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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Zhao T, Murphy RF. Automated learning of generative models for subcellular location: building blocks for systems biology. Cytometry A. 2007;71:978–90.
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.
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.
Tidwell J. Designing Interfaces. O’Reilly; 2007.
Carpenter AE, Jones TR, LamprechtMR, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2007; p. 7:R100.
M¨oller B, Posch S. A framework unifying the development of image analysis algorithms and associated user interfaces. Proc MVA. 2013; p. 447–50.
Kass M, Witkin A, Terzopoulus D. Snakes: active contour models. Int J of Comput Vis. 1988; p. 321–31.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Franz, D., Huettmayer, H., Stamminger, M., Wiesmann, V., Wittenberg, T. (2015). The Cell-Shape-Wizard. In: Handels, H., Deserno, T., Meinzer, HP., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2015. Informatik aktuell. Springer Vieweg, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-46224-9_59
Download citation
DOI: https://doi.org/10.1007/978-3-662-46224-9_59
Published:
Publisher Name: Springer Vieweg, Berlin, Heidelberg
Print ISBN: 978-3-662-46223-2
Online ISBN: 978-3-662-46224-9
eBook Packages: Computer Science and Engineering (German Language)