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Fungal Networks

Microbial biology: investigating critical developmental transitions via imaging, image analysis and mathematical modelling

Saprotrophic fungi are critical in ecosystem biology as they are the only organisms capable of complete degradation of wood in temperate forests. These fungi form extensive interconnected mycelial networks that scavenge efficiently for scarce resources in a heterogeneous environment. The architecture of the network continuously adapts to local nutritional cues, damage or predation, through growth, branching, fusion or regression. Such biological networks, honed by evolution, may exemplify potential solutions to real-world compromises between cost, coverage, resilience and persistence. We need to be able to automatically analyse the dynamic network architecture to evaluate their performance efficiently. We propose an image processing approach for fungal network segmentation and graph-based analysis.

An image of a fungal network.

Collaborators:

  • Dr Mark Fricker, Department of Plant Sciences, University of Oxford, UK
  • Dr Vicente Grau, Oxford e-Research Centre, University of Oxford, UK
  • Prof. David Gavaghan, Oxford University Computing Laboratory, University of Oxford, UK

Publications:

  • [2012,article] bibtex
    B. Obara, M. Fricker, and V. Grau, "A bioimage informatics approach to automatically extract complex fungal networks," Bioinformatics, vol. 28, iss. 18, pp. 2374-2381, 2012.
    @article{Obara2012f,
      author = {Boguslaw Obara and Mark Fricker and Vicente Grau},
      title = {A bioimage informatics approach to automatically extract complex fungal networks},
      journal = {Bioinformatics},
      volume = {28},
      number = {18},
      pages = {2374-2381},
      year = {2012}
    }
  • [2012,article] bibtex
    B. Obara, M. Fricker, D. Gavaghan, and V. Grau, "Contrast-independent curvilinear structure detection in biomedical images," IEEE Transactions on Image Processing, vol. 21, iss. 5, pp. 2572-2581, 2012.
    @article{Obara2012b,
      author = {Boguslaw Obara and Mark Fricker and David Gavaghan and Vicente Grau},
      title = {Contrast-independent curvilinear structure detection in biomedical images},
      journal = {IEEE Transactions on Image Processing},
      volume = {21},
      number = {5},
      pages = {2572-2581},
      year = {2012}
    }
  • [2012,article] bibtex
    L. Heaton, B. Obara, V. Grau, N. Jones, T. Nakagaki, L. Boddy, and M. Fricker, "Analysis of fungal networks," Fungal Biology Reviews, vol. 26, iss. 1, pp. 12-29, 2012.
    @article{Heaton2012,
      author = {Luke Heaton and Boguslaw Obara and Vincente Grau and Nick Jones and Toshiyuki Nakagaki and Lynne Boddy and Mark Fricker},
      title = {Analysis of fungal networks},
      journal = {Fungal Biology Reviews},
      volume = {26},
      number = {1},
      pages = {12-29},
      year = {2012}
    }
  • [2012,inproceedings] bibtex
    B. Obara, M. Fricker, and V. Grau, "Bioimage informatics for biomedical networks," in Oxford Systems Biology: Building Networks and Bridging Scales, Oxford, UK, 2012.
    @inproceedings{Obara2012e,
      author = {Boguslaw Obara and Mark Fricker and Vicente Grau},
      title = {Bioimage informatics for biomedical networks},
      booktitle = {Oxford Systems Biology: Building Networks and Bridging Scales},
      address = {Oxford, UK},
      month = {19-21 June},
      year = {2012}
    }
  • [2012,inproceedings] bibtex
    B. Obara, M. Fricker, and V. Grau, "Local phase approaches to extract biomedical networks," in IEEE International Symposium on Biomedical Imaging, Barcelona, Spain, 2012, pp. 1796-1799.
    @inproceedings{Obara2012d,
      author = {Boguslaw Obara and Mark Fricker and Vicente Grau},
      title = {Local phase approaches to extract biomedical networks},
      booktitle = {IEEE International Symposium on Biomedical Imaging},
      address = {Barcelona, Spain},
      pages = {1796-1799},
      month = {2-5 May},
      year = {2012}
    }
  • [2012,inproceedings] bibtex
    B. Obara, M. Fricker, and V. Grau, "Coherence enhancing diffusion filtering based on the Phase Congruency Tensor," in IEEE International Symposium on Biomedical Imaging, Barcelona, Spain, 2012, pp. 202-205.
    @inproceedings{Obara2012c,
      author = {Boguslaw Obara and Mark Fricker and Vicente Grau},
      title = {Coherence enhancing diffusion filtering based on the {Phase Congruency Tensor}},
      booktitle = {IEEE International Symposium on Biomedical Imaging},
      address = {Barcelona, Spain},
      pages = {202-205},
      month = {2-5 May},
      year = {2012}
    }
  • [2012,inproceedings] bibtex
    B. Obara, M. Fricker, and V. Grau, "Contrast independent detection of branching points in network-like structures," in SPIE Medical Imaging, San Diego, CA, USA, 2012, p. 83141.
    @inproceedings{Obara2012a,
      author = {Boguslaw Obara and Mark Fricker and Vicente Grau},
      title = {Contrast independent detection of branching points in network-like structures},
      booktitle = {SPIE Medical Imaging},
      address = {San Diego, CA, USA},
      pages = {83141L},
      month = {4-9 February},
      year = {2012}
    }