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Computing and Visualization in Science

, Volume 17, Issue 4, pp 151–166 | Cite as

Computational modeling of fluorescence loss in photobleaching

  • Christian V. HansenEmail author
  • Hans J. Schroll
  • Daniel Wüstner
Article

Abstract

Fluorescence loss in photobleaching (FLIP) is a modern microscopy method for visualization of transport processes in living cells. Although FLIP is widespread, an automated reliable analysis of image data is still lacking. This paper presents a framework for modeling and simulation of FLIP sequences as reaction–diffusion systems on segmented cell images. The cell geometry is extracted from microscopy images using the Chan–Vese active contours algorithm (IEEE Trans Image Process 10(2):266–277, 2001). The PDE model is subsequently solved by the automated Finite Element software package FEniCS (Logg et al. in Automated solution of differential equations by the finite element method. Springer, Heidelberg, 2012). The flexibility of FEniCS allows for spatially resolved reaction diffusion coefficients in two (or more) spatial dimensions.

Keywords

Discontinuous Galerkin Method Fluorescence Recovery After Photobleaching Fluorescence Recovery After Photobleaching Experiment Fluorescence Loss Bleaching Area 
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.

Notes

Acknowledgments

The authors want to thank Niels Christian Overgaard from Lund University for introducing us to level set methods in image segmentation.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Christian V. Hansen
    • 1
    Email author
  • Hans J. Schroll
    • 1
  • Daniel Wüstner
    • 2
  1. 1.Department of Mathematics and Computer ScienceUniversity of Southern DenmarkOdense MDenmark
  2. 2.Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark

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