Volume 14 Supplement 1

Abstracts from the Twenty Second Annual Computational Neuroscience Meeting: CNS*2013

Open Access

Interactive visualization of brain-scale spiking activity

  • Christian Nowke1, 5Email author,
  • Bernd Hentschel1, 5,
  • Torsten Kuhlen1, 5,
  • Maximilian Schmidt2, 5,
  • Sacha J van Albada2, 5,
  • Jochen M Eppler2, 5,
  • Rembrandt Bakker2, 3, 5 and
  • Markus Diesmann2, 4, 5
BMC Neuroscience201314(Suppl 1):P110

DOI: 10.1186/1471-2202-14-S1-P110

Published: 8 July 2013

In recent years, the simulation of spiking neural networks has advanced in terms of both simulation technology [1, 2] and knowledge about neuroanatomy [3, 4]. Due to these advances, it is now possible to run simulations at the brain scale [5, 6], which produce an unprecedented amount of data to be analyzed and understood by researchers.

To aid computational neuroscientists with the development of models and especially with the visual inspection and selection of data for analysis, we developed VisNEST [7], a tool for the combined visualization of simulated spike data and anatomy. This provides a rapid overview of the relationship between structure and activity. VisNEST currently uses spike data from the neural simulation tool NEST [1] and geometry from the Scalable Brain Atlas [4], but is not limited to these tools.

In our contribution we will present VisNEST using a Picasso 3D system, which allows users to interactively investigate and explore the simulated data from a large-scale model of 32 vision-related areas of the macaque [6]. The system is equipped with infrared tracking and uses passive glasses to render the image for the user standing in front of the screen.
Figure 1

Main view of the simulated activity data. The mean spiking activity of the different areas is shown by color. The optional dot plot shows the spikes from the currently selected area.



Partially supported by the Helmholtz Association: HASB and portfolio theme SMHB, the Next-Generation Supercomputer Project of MEXT, EU Grant 269921 (BrainScaleS), by the VSR computation time grant JINB33 on the JUGENE and JUQUEEN supercomputers in Jülich, the Jülich-Aachen Research Alliance (JARA) and by the Excellence Initiative of the German federal and state governments.

Authors’ Affiliations

Virtual Reality Group, RWTH Aachen University
Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), Jülich Research Centre
Donders Institute for Brain, Cognition and Behavior, Radboud University
Medical Faculty, RWTH Aachen University
JARA - High-Performance Computing, RWTH Aachen University


  1. Gewaltig MO, Diesmann M: NEST (NEural Simulation Tool). Scholarpedia. 2007, 2 (4): 1430.-10.4249/scholarpedia.1430.View ArticleGoogle Scholar
  2. Helias M, Kunkel S, Masumoto G, Igarashi J, Eppler JE, Ishii S, Fukai T, Morrison A, Diesmann M: Supercomputers ready for use as discovery machines for neuroscience. Front Neuroinform. 2012, 6: 26-PubMed CentralView ArticlePubMedGoogle Scholar
  3. Stephan KE, Kamper L, Bozkurt A, Burns GAPC, Young MP, Kötter R: Advanced database methodology for the collation of connectivity data on the macaque brain (CoCoMac). Phil Trans R Soc Lond B. 2001, 356-Google Scholar
  4. Bakker R, Bezgin G: Scalable brain atlas. 2012, [http://scalablebrainatlas.incf.org/]Google Scholar
  5. Potjans T, Diesmann M: The cell-type specific cortical microcircuit: relating structure and activity in a full-scale spiking network model. Cerebral Cortex. 2012, doi:10.1093/cercor/bhs358Google Scholar
  6. Schmidt M, van Albada S, Bakker R, Diesmann M: Toward a spiking multi-area network model of macaque visual cortex. Tenth Göttingen Meeting of the German Neuroscience Society. 2013Google Scholar
  7. Nowke C, Hentschel B, Kuhlen T, Eppler JM, van Albada S, Bakker R, Diesmann M, Schmidt M: VisNest - Interactive Analysis of Neural Activity Data. IEEE VIS 2012 Poster Abstracts. 2012Google Scholar


© Nowke et al; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.