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Bildverarbeitung für die Medizin 2011 pp 34–38Cite as

3D Segmentation and Quantification of Mouse Embryonic Stem Cells in Fluorescence Microscopy Images

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Part of the book series: Informatik aktuell ((INFORMAT))

Abstract

We present an automatic approach for 3D segmentation of mouse embryonic stem cell nuclei based on level set active contours. Due to the specific properties of these cells, standard methods for cell nucleus segmentation and splitting of cell clusters cannot be applied. Our segmentation approach combines information from two different channels, which represent the nuclear region and the nuclear membrane, respectively. Moreover, we perform segmentation of gene loci within two other channels which enables single cell quantification of gene distances.

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References

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Author information

Authors and Affiliations

  1. Dept. Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, University of Heidelberg, BIOQUANT, IPMB, and DKFZ Heidelberg, Heidelberg, Germany

    N. Harder, R. Eils & K. Rohr

  2. Spector Lab, Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, NY, USA

    M. Bodnar & D. L. Spector

Authors
  1. N. Harder
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  2. M. Bodnar
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  3. R. Eils
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  4. D. L. Spector
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  5. K. Rohr
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Corresponding author

Correspondence to N. Harder .

Editor information

Editors and Affiliations

  1. , Institut für Medizinische Informatik, Universität zu Lübeck, Ratzeburger Allee 160, Lübeck, 23562, Germany

    Heinz Handels

  2. , Institut für Medizinische Informatik, Universität Lübeck, Ratzeburger Allee 160, Lübeck, 23538, Germany

    Jan Ehrhardt

  3. Inst. Medizinische Informatik, RWTH Aachen, Pauwelsstr. 30, Aachen, 52074, Germany

    Thomas M. Deserno

  4. Abt. Med./Biol.Inform./H0100, Deutsches Krebsforschungzentrum (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany

    Hans-Peter Meinzer

  5. Charité Campus Benjamin Franklin, Inst. Medizinische Informatik,, Universitätsklinikum Berlin, Hindenburgdamm 30, Berlin, 12200, Berlin, Germany

    Thomas Tolxdorff

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© 2011 Springer-Verlag Berlin Heidelberg

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Harder, N., Bodnar, M., Eils, R., Spector, D., Rohr, K. (2011). 3D Segmentation and Quantification of Mouse Embryonic Stem Cells in Fluorescence Microscopy Images. In: Handels, H., Ehrhardt, J., Deserno, T., Meinzer, HP., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2011. Informatik aktuell. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-19335-4_9

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