A deep learning-based algorithm for 2-D cell segmentation in microscopy images View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Yousef Al-Kofahi, Alla Zaltsman, Robert Graves, Will Marshall, Mirabela Rusu

ABSTRACT

BACKGROUND: Automatic and reliable characterization of cells in cell cultures is key to several applications such as cancer research and drug discovery. Given the recent advances in light microscopy and the need for accurate and high-throughput analysis of cells, automated algorithms have been developed for segmenting and analyzing the cells in microscopy images. Nevertheless, accurate, generic and robust whole-cell segmentation is still a persisting need to precisely quantify its morphological properties, phenotypes and sub-cellular dynamics. RESULTS: We present a single-channel whole cell segmentation algorithm. We use markers that stain the whole cell, but with less staining in the nucleus, and without using a separate nuclear stain. We show the utility of our approach in microscopy images of cell cultures in a wide variety of conditions. Our algorithm uses a deep learning approach to learn and predict locations of the cells and their nuclei, and combines that with thresholding and watershed-based segmentation. We trained and validated our approach using different sets of images, containing cells stained with various markers and imaged at different magnifications. Our approach achieved a 86% similarity to ground truth segmentation when identifying and separating cells. CONCLUSIONS: The proposed algorithm is able to automatically segment cells from single channel images using a variety of markers and magnifications. More... »

PAGES

365

References to SciGraph publications

  • 2015-05. Deep learning in NATURE
  • 1993-12. Detecting salient blob-like image structures and their scales with a scale-space primal sketch: A method for focus-of-attention in INTERNATIONAL JOURNAL OF COMPUTER VISION
  • 2017-12. An objective comparison of cell-tracking algorithms in NATURE METHODS
  • 2006-04. CellProfiler: image analysis software for identifying and quantifying cell phenotypes in GENOME BIOLOGY
  • 2006. Cell Segmentation Using Coupled Level Sets and Graph-Vertex Coloring in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION – MICCAI 2006
  • 2015. U-Net: Convolutional Networks for Biomedical Image Segmentation in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION – MICCAI 2015
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12859-018-2375-z

    DOI

    http://dx.doi.org/10.1186/s12859-018-2375-z

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30285608


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