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Methods ARTICLE

Visualizing neuronal network connectivity with connectivity pattern tables

Eilen Nordlie¹ and Hans Ekkehard Plesser^1,2,3*

Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Ås, Norway

Center for Biomedical Computing, Simula Research Laboratory, Lysaker, Norway

RIKEN Brain Science Institute, Wako-shi, Saitama, 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, visualization, projection, population

Citation:

Nordlie E and Plesser HE (2010) Visualizing neuronal network connectivity with connectivity pattern tables. Front. Neuroinform. 3,39:1-15. doi: 10.3389/neuro.11.039.2009

Received:

13 October 2009;

Paper pending published:

11 January 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, Centre National de la Recherche Scientifi que, France
Tom Binzegger, University of Newcastle upon Tyne, UK

© 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, Department of Mathematical Sciences and Technology, IMT, Norwegian University of Life Sciences (UMB), P.O. Box 5003, NO-1432 Ås, Norway. e-mail: hans.ekkehard.plesser@umb.no