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Methods Article
Visualizing neuronal network connectivity with connectivity pattern tables
Eilen Nordlie 1 and Hans Ekkehard Plesser 1, 2, 3*
1
Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
2
Center for Biomedical Computing, Simula Research Laboratory, Norway
3
RIKEN Brain Science Institute, Japan
Complex ideas are best conveyed through well-designed illustrations. Up to now, computational neuroscientists have mostly relied on box-and-arrow diagrams of even complex neuronal networks, often using ad hoc notations with conflicting use of symbols from paper to paper. This significantly impedes the communication of ideas in neuronal network modeling. We present here Connectivity Pattern Tables (CPTs) as a clutter-free visualization of connectivity in large neuronal networks containing two-dimensional populations of neurons. CPTs can be generated automatically from the same script code used to create the actual network in the NEST simulator. Through aggregation, CPTs can be viewed at different levels, providing either full detail or summary information. We also provide the open source ConnPlotter tool as a means to create connectivity pattern tables.
Keywords: neuronal network, connectivity, projection, population, visualization
Copyright: © 2010 Nordlie and Plesser. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
*Correspondence: Hans Ekkehard Plesser, Norwegian University of Life Sciences, Dept. of Mathematical Sciences and Technology, PO Box 5003, 1432 Aas, Norway, hans.ekkehard.plesser@umb.no
Citation: Nordlie E and Plesser H (2010) Visualizing neuronal network connectivity with connectivity pattern tables. Front. Neuroinform. 3:39. doi:10.3389/neuro.11.039.2009
Received: 13 October 2009; Paper pending published: 01 November 2009; Accepted: 16 December 2009; Published online: 29 January 2010.
Edited by:
Anders Lansner, KTH, Sweden
Reviewed by:
Mikael Djurfeldt, KTH, Sweden
Andrew P. Davison, CNRS, France
Tom Binzegger, University of Newcastle upon Tyne, UK
Andrew P. Davison, CNRS, France
Tom Binzegger, University of Newcastle upon Tyne, UK
*Correspondence: Hans Ekkehard Plesser, Norwegian University of Life Sciences, Dept. of Mathematical Sciences and Technology, PO Box 5003, 1432 Aas, Norway, hans.ekkehard.plesser@umb.no


