A flexible and robust approach for segmenting cell nuclei from 2D microscopy images using supervised learning and template matching

Authors

  • Cheng Chen,

    1. Center for Bioimage Informatics, Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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  • Wei Wang,

    1. Center for Bioimage Informatics, Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
    2. Department of Electronic and Information Engineering, School of Electronic and Information Engineering, Beijing Jiaotong University, Beijing, China
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  • John A. Ozolek,

    1. Department of Pathology, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15201
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  • Gustavo K. Rohde

    Corresponding author
    1. Center for Bioimage Informatics, Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
    2. Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
    3. Computational Biology Program, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
    • Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213.
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Abstract

We describe a new supervised learning-based template matching approach for segmenting cell nuclei from microscopy images. The method uses examples selected by a user for building a statistical model that captures the texture and shape variations of the nuclear structures from a given dataset to be segmented. Segmentation of subsequent, unlabeled, images is then performed by finding the model instance that best matches (in the normalized cross correlation sense) local neighborhood in the input image. We demonstrate the application of our method to segmenting nuclei from a variety of imaging modalities, and quantitatively compare our results to several other methods. Quantitative results using both simulated and real image data show that, while certain methods may work well for certain imaging modalities, our software is able to obtain high accuracy across several imaging modalities studied. Results also demonstrate that, relative to several existing methods, the template-based method we propose presents increased robustness in the sense of better handling variations in illumination, variations in texture from different imaging modalities, providing more smooth and accurate segmentation borders, as well as handling better cluttered nuclei. © 2013 International Society for Advancement of Cytometry

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