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Cytoskeletal Networks

Data driven approaches to understanding cytoskeletal network complexity

A 3D/4D cytoskeletal network may contain thousands of nodes and connections, in specific but variable geometric organisations which vary with time. Such data exceeds the capacity of human analysis, creating a barrier, which can only be overcome with robust, automated image analysis and informatics tools to extract, characterise and model networks. Having such topological characteristics, some key open questions that can then be explored are:

  • How are topology and function related to each other?
  • What are the underlying dynamics that shape the network patterns?
  • How important is the formation of alternative paths through the network via crosslinks?
  • How does the network evolve to confer high robustness?
  • How local responsive changes affect the global network?

3D actin filament network.

3D actin filament network.

Collaborators:

  • Dr Martin Goldberg, School of Biological & Biomedical Sciences, University of Durham, UK
  • Dr Tim Hawkins, Microscopy & Bioimaging, University of Durham, UK
  • Prof. Patrick J. Hussey, School of Biological & Biomedical Sciences, University of Durham, UK
  • Prof. Roy Quinlan, School of Biological & Biomedical Sciences, University of Durham, UK
  • Prof. David Ehrhardt, Carnegie Institution for Science, Stanford University, USA

Publications:

[Submitted]

  • [2017,article] bibtex
    C. Sazak, C. J. Nelson, and B. Obara, "The multiscale bowler-hat transform for blood vessel enhancement in retinal images," IEEE Transactions on Medical Imaging, 2017.
    @article{Cigdem2017R,
      author = {Cigdem Sazak and Carl J. Nelson and Boguslaw Obara},
      title = {The multiscale bowler-hat transform for blood vessel enhancement in retinal images},
      journal = {IEEE Transactions on Medical Imaging},
      year = {2017}
    }
  • [2017,inproceedings] bibtex
    C. Sazak and B. Obara, "Contrast-independent curvilinear structure enhancement in 3D biomedical images," in IEEE International Symposium on Biomedical Imaging, Melbourne, Australia, 2017, pp. 1165-1168.
    @inproceedings{Sazak2017,
      author = {Cigdem Sazak and Boguslaw Obara},
      title = {Contrast-independent curvilinear structure enhancement in {3D} biomedical images},
      booktitle = {IEEE International Symposium on Biomedical Imaging},
      address = {Melbourne, Australia},
      month = {18-21 April},
      pages = {1165-1168},
      year = {2017}
    }