Automated analysis of Physarum network structure and dynamics

We describe software tools to extract the network architecture from time-series of Physarum development using intensity-independent, phase-congruency tensors and watershed segmentation to give a set of weighted adjacency matrices with the physical size of each tube. The network can also be interrogated to map the phase, amplitude and frequency of the oscillations using windowed Fourier techniques.

[1]  A. Tero,et al.  Rules for Biologically Inspired Adaptive Network Design , 2010, Science.

[2]  S. Garnier,et al.  Decision-making without a brain: how an amoeboid organism solves the two-armed bandit , 2016, Journal of The Royal Society Interface.

[3]  Guy Theraulaz,et al.  Efficiency and robustness in ant networks of galleries , 2004 .

[4]  Sang Hoon Lee,et al.  Mesoscale analyses of fungal networks as an approach for quantifying phenotypic traits , 2014, bioRxiv.

[5]  Michael T. Gastner,et al.  Shape and efficiency in spatial distribution networks , 2006 .

[6]  M. Beekman,et al.  Brainless but Multi-Headed: Decision Making by the Acellular Slime Mould Physarum polycephalum. , 2015, Journal of molecular biology.

[7]  M. Fricker,et al.  Analysis of fungal networks , 2012 .

[8]  Adrian Neumann,et al.  NEFI: Network Extraction From Images , 2015, Scientific Reports.

[9]  Svetha Venkatesh,et al.  On the classification of image features , 1990, Pattern Recognit. Lett..

[10]  Werner Baumgarten,et al.  Computational algorithms for extraction and analysis of two-dimensional transportation networks , 2012 .

[11]  V. Latora,et al.  Structural properties of planar graphs of urban street patterns. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[12]  P. Maini,et al.  Growth-induced mass flows in fungal networks , 2010, Proceedings of the Royal Society B: Biological Sciences.

[13]  M. Fricker,et al.  Fourier-based spatial mapping of oscillatory phenomena in fungi. , 2007, Fungal genetics and biology : FG & B.

[14]  Herbert Edelsbrunner,et al.  Hierarchical Ordering of Reticular Networks , 2011, PloS one.

[15]  Toshiyuki Nakagaki,et al.  A Method Inspired by Physarum for Solving the Steiner Problem , 2010, Int. J. Unconv. Comput..

[16]  Edward H. Adelson,et al.  The Design and Use of Steerable Filters , 1991, IEEE Trans. Pattern Anal. Mach. Intell..

[17]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[18]  P. Maini,et al.  Advection, diffusion, and delivery over a network. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[19]  Guy Theraulaz,et al.  Topological patterns in street networks of self-organized urban settlements , 2006 .

[20]  Boguslaw Obara,et al.  A bioimage informatics approach to automatically extract complex fungal networks , 2012, Bioinform..

[21]  Toshiyuki Nakagaki,et al.  Adaptive Biological Networks , 2009 .

[22]  Christina Oettmeier,et al.  Structuring precedes extension in percolating Physarum polycephalum networks , 2015, Nano Commun. Networks.

[23]  Robyn A. Owens,et al.  Feature detection from local energy , 1987, Pattern Recognit. Lett..

[24]  A. Takamatsu,et al.  Characterization of Adaptation by Morphology in a Planar Biological Network of Plasmodial Slime Mold , 2011 .

[25]  Takaya Saito,et al.  The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets , 2015, PloS one.

[26]  M. Fricker,et al.  Experimental models for Murray’s law , 2017 .

[27]  Peng-Lang Shui,et al.  Noise-robust edge detector combining isotropic and anisotropic Gaussian kernels , 2012, Pattern Recognit..

[28]  Peter Kovesi,et al.  Image Features from Phase Congruency , 1995 .

[29]  Lynne Boddy,et al.  Fungal network responses to grazing. , 2010, Fungal genetics and biology : FG & B.

[30]  Toshiyuki Nakagaki,et al.  Amoebae anticipate periodic events. , 2008, Physical review letters.

[31]  Jian Sun,et al.  Guided Image Filtering , 2010, ECCV.

[32]  Eleni Katifori,et al.  Quantifying Loopy Network Architectures , 2011, PloS one.

[33]  L Boddy,et al.  Imaging complex nutrient dynamics in mycelial networks , 2008, Journal of microscopy.

[34]  Carsten Steger,et al.  An Unbiased Detector of Curvilinear Structures , 1998, IEEE Trans. Pattern Anal. Mach. Intell..

[35]  Christina Oettmeier,et al.  Physarum polycephalum percolation as a paradigm for topological phase transitions in transportation networks. , 2012, Physical review letters.

[36]  Madeleine Beekman,et al.  Solving the Towers of Hanoi – how an amoeboid organism efficiently constructs transport networks , 2013, Journal of Experimental Biology.

[37]  Humberto Bustince,et al.  Quantitative error measures for edge detection , 2013, Pattern Recognit..

[38]  P Kovesi,et al.  Phase congruency: A low-level image invariant , 2000, Psychological research.

[39]  Fernand Meyer,et al.  Topographic distance and watershed lines , 1994, Signal Process..

[40]  M. Fricker,et al.  Biological solutions to transport network design , 2007, Proceedings of the Royal Society B: Biological Sciences.

[41]  A. Dussutour,et al.  Slime mold uses an externalized spatial “memory” to navigate in complex environments , 2012, Proceedings of the National Academy of Sciences.

[42]  M. Hauser,et al.  Functional organization of the vascular network of Physarum polycephalum , 2013, Physical biology.

[43]  Alejandro F. Frangi,et al.  Muliscale Vessel Enhancement Filtering , 1998, MICCAI.

[44]  V Latora,et al.  Efficient behavior of small-world networks. , 2001, Physical review letters.

[45]  M. Melamed.  Detection , 2021, SETI: Astronomy as a Contact Sport.

[46]  M. Brenner,et al.  Random network peristalsis in Physarum polycephalum organizes fluid flows across an individual , 2013, Proceedings of the National Academy of Sciences.

[47]  T F Sherman,et al.  On connecting large vessels to small. The meaning of Murray's law , 1981, The Journal of general physiology.

[48]  Werner Baumgarten,et al.  Plasmodial vein networks of the slime mold Physarum polycephalum form regular graphs. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[49]  Bernard De Baets,et al.  Unsupervised ridge detection using second order anisotropic Gaussian kernels , 2015, Signal Process..

[50]  C. D. Murray.  THE PHYSIOLOGICAL PRINCIPLE OF MINIMUM WORK , 1931, The Journal of general physiology.

[51]  Jukka-Pekka Onnela,et al.  Taxonomies of networks from community structure. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[52]  Pierre Soille,et al.  Morphological Image Analysis: Principles and Applications , 2003 .

[53]  Michael P Brenner,et al.  Pruning to Increase Taylor Dispersion in Physarum polycephalum Networks. , 2016, Physical review letters.

[54]  E Meijering,et al.  Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images , 2004, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[55]  P. Haggett.  Network Analysis In Geography , 1971 .