IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0036575.html
   My bibliography  Save this article

Parameter-Free Binarization and Skeletonization of Fiber Networks from Confocal Image Stacks

Author

Listed:
  • Patrick Krauss
  • Claus Metzner
  • Janina Lange
  • Nadine Lang
  • Ben Fabry

Abstract

We present a method to reconstruct a disordered network of thin biopolymers, such as collagen gels, from three-dimensional (3D) image stacks recorded with a confocal microscope. The method is based on a template matching algorithm that simultaneously performs a binarization and skeletonization of the network. The size and intensity pattern of the template is automatically adapted to the input data so that the method is scale invariant and generic. Furthermore, the template matching threshold is iteratively optimized to ensure that the final skeletonized network obeys a universal property of voxelized random line networks, namely, solid-phase voxels have most likely three solid-phase neighbors in a neighborhood. This optimization criterion makes our method free of user-defined parameters and the output exceptionally robust against imaging noise.

Suggested Citation

  • Patrick Krauss & Claus Metzner & Janina Lange & Nadine Lang & Ben Fabry, 2012. "Parameter-Free Binarization and Skeletonization of Fiber Networks from Confocal Image Stacks," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-8, May.
    • Handle: RePEc:plo:pone00:0036575
    DOI: 10.1371/journal.pone.0036575
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0036575
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0036575&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0036575?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0036575. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.