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Deep Segmentation of Bacteria at Different Stages of the Life Cycle

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Book cover Bildverarbeitung für die Medizin 2020

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

Zusammenfassung

Segmentation of bacteria in live cell microscopy image sequences is a crucial task to gain insights into molecular processes. A main challenge is that some bacteria strongly change their appearance during the life cycle as response to fluctuations in environmental conditions. We present a novel deep learning method with shape-based weighting of the loss function to accurately segment bacteria during different stages of the life cycle. We evaluate the performance of the method for live cell microscopy images of Bacillus subtilis bacteria with strong changes during the life cycle.

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Author information

Authors and Affiliations

  1. Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University Im Neuenheimer Feld 267, Heidelberg, Deutschland

    Roman Spilger, Tobias Schwackenhofer & Karl Rohr

  2. BioQuant, Center for Molecular Biology (ZMBH),, Heidelberg University, Heidelberg, Deutschland

    Charlotte Kaspar & Ilka Bischofs

  3. Max Planck Institute for Terrestrial Microbiology, Marburg, Deutschland

    Charlotte Kaspar & Ilka Bischofs

Authors
  1. Roman Spilger
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  2. Tobias Schwackenhofer
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  3. Charlotte Kaspar
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  4. Ilka Bischofs
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  5. Karl Rohr
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Corresponding author

Correspondence to Roman Spilger .

Editor information

Editors and Affiliations

  1. Institut für Medizinische Informatik, Charité - Universitätsmedizin Berlin, Berlin, Germany

    Thomas Tolxdorff

  2. Peter L. Reichertz Institut für Medizinische Informatik, Technische Universität Braunschweig, Braunschweig, Germany

    Thomas M. Deserno

  3. Institut für Medizinische Informatik, Universität zu Lübeck, Lübeck, Germany

    Heinz Handels

  4. Lehrstuhl für Mustererkennung, Friedrich-Alexander-Universität, Erlangen, Germany

    Andreas Maier

  5. Medical Image Computing, E230, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany

    Klaus H. Maier-Hein

  6. Fakultät für Informatik und Mathematik, Ostbayerische Technische Hochschule Regensburg, Regensburg, Germany

    Christoph Palm

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© 2020 Springer Fachmedien Wiesbaden GmbH, ein Teil von Springer Nature

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Spilger, R., Schwackenhofer, T., Kaspar, C., Bischofs, I., Rohr, K. (2020). Deep Segmentation of Bacteria at Different Stages of the Life Cycle. In: Tolxdorff, T., Deserno, T., Handels, H., Maier, A., Maier-Hein, K., Palm, C. (eds) Bildverarbeitung für die Medizin 2020. Informatik aktuell. Springer Vieweg, Wiesbaden. https://doi.org/10.1007/978-3-658-29267-6_2

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