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Cell shape recognition and segmentation in fluorescence microscopy images.

doi: 10.6062/jcis.2012.03.02.0055(Free PDF)


Anielski A., Pfannes E. K. B., and Beta, C.


Many cellular processes involve the translocation of proteins from the cytosolic region to the cortex of the cell and vice versa. The dynamics of such processes is typically investigated by fluorescence imaging of GFP-labeled versions of these proteins. Quantitative analysis of the resulting fluorescence images requires image segmentation procedures that identify the cell within the image and subsequently divide the cell into a cytosolic and a cortical region to monitor the temporal evolution of the fluorescence signals within these parts of the cell separately. Here, we present an image segmentation protocol that we have developed for this type of data analysis. It consists of noise reduction, normalization, and thresholding steps to generate masks that define the cytosolic and the cortical regions of a cell. Based on these masks, the desired fluorescence signals can be extracted from the confocal microscopy images.


fluorescence microscopy, image processing, Dictyostelium.


[1] GOLDMAN RD, SWEDLOW JR & SPECTOR DL (Eds.). 2010. Live Cell Imaging. Cold Spring Harbor Laboratory Press.

[2] ISHIKAWA-ANKERHOLD HC, ANKERHOLD R & DRUMMEN GPC. 2012. Advanced Fluorescence Microscopy Techniques - FRAP, FLIP, FLAP, FRET and FLIM. Molecules, 17: 4047-4132.

[3] HELL SW. 2007. Far-Field Optical Nanoscopy. Science, 316: 1153-1158.

[4] http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/bretschneider/quimp/

[5] http://rsbweb.nih.gov/ij/

[6] DORMANN D, LIBOTTE T, WEIJER CJ & BRETSCHNEIDER T. Simultaneous Quantification of Cell Motility and Protein-Membrane-Association Using Active Contours. Cell Motility and Specificity of Three cAMP Receptors in Dictyostelium. Journal of the Cytoskeleton, 52: 221-230.

[7] BOSGRAAF L, VAN HAASTERT PJM & BRETSCHNEIDER T.2009 Analysis of Cell Movement by Simultaneous Quantification of Local Membrane Displacement and Fluorescent Intensities Using Quimp2. Cell Motility and the Cytoskeleton, 66: 156-165.

[8] MACHACEK M & DANUSER G. 2006. Morphodynamic Profiling of Protrusion Phenotypes. Biophysical Journal, 90: 1439-1452.

[9] SCHNEIDER N, WEBER I, FAIX J, PRASSER J, MULLER-TAUBEN-BERGER A, KOHLER J, BURGHARDT E, GERISCH G & MARRIOTT G. 2003. A Lim Protein Involved in the Progression of Cytokine-sis and Regulation of the Mitotic Spindle. Cell Motility and the Cytoskeleton, 56: 130-139.

[10] YYUMURA S & FUKUI Y. 1985. Reversible cyclic AMP-dependent change in the distribution of myosin thick filaments in Dictyostelium. Nature, 314: 194-196.

[11] http://www.mathworks.de/help/techdoc/

[12] VAN HAASTERT PJM & KIEN E. 1983. Binding of cAMP Derivatives to Dictyostelium discoideum Cells. Journal of Biological Chemistry, 258: 9636-9642.

[13] OHNSON RL, VAN HAASTERT PJM, KIMMEL AR, SAXE III CL, JASTORFF B & DEVREOTES PN. 1992. The Cyclic Nucleotide Specificity of Three cAMP Receptors in Dictyostelium. Journal of Biological Chemistry, 267: 4600-4607.

[14] GOELDNER M & GIVENS R (Eds.). 2005. Dynamic Studies in Biology: Phototriggers, Photoswitches an Caged Biomolecules. Wiley-VCH.

[15] ETZRODT M, ISHIKAWA HCF, DALOUS J, MULLER-TAUBEN-BERGER A, BRETSCHNEIDER T & GERISCH G, 2006. Time-resolved responses to chemoattractant, characteristics of the front and tail of Dictyostelium cells. FEBS Letters, 580: 6707-6713.

[17] DOS ANJOS A & SHAHBAZKIA HR. 2008. Bi-level image thresholding - A fast method. Biosignals 2008. Proceedings, 70-76.

[18] CHAN TF & VESE LA. 2001. Active Contours Without Edges. IEEE Transactions on Image Processing, 10: 266-277.


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