CDeep3M-Plug-and-Play cloud-based deep learning for image segmentation.

Journal: Nature methods
Published Date: Aug 31, 2018

Abstract

As biomedical imaging datasets expand, deep neural networks are considered vital for image processing, yet community access is still limited by setting up complex computational environments and availability of high-performance computing resources. We address these bottlenecks with CDeep3M, a ready-to-use image segmentation solution employing a cloud-based deep convolutional neural network. We benchmark CDeep3M on large and complex two-dimensional and three-dimensional imaging datasets from light, X-ray, and electron microscopy.

Authors

  • Matthias G Haberl
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA. haberlmatt@gmail.com.
  • Christopher Churas
    National Biomedical Computation Resource, University of California San Diego, La Jolla, CA, USA.
  • Lucas Tindall
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Daniela Boassa
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Sébastien Phan
    National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California San Diego, La Jolla, CA 92039, USA.
  • Eric A Bushong
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Matthew Madany
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Raffi Akay
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Thomas J Deerinck
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Steven T Peltier
    National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.
  • Mark H Ellisman
    National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California San Diego, La Jolla, CA 92039, USA.

Keywords

External Resources

Popular Topics
Recent Journals