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Interactive visualization of brain-scale spiking activity

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
figure1

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.

References

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    Gewaltig MO, Diesmann M: NEST (NEural Simulation Tool). Scholarpedia. 2007, 2 (4): 1430.-10.4249/scholarpedia.1430.

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    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-

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    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-

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    Bakker R, Bezgin G: Scalable brain atlas. 2012, [http://scalablebrainatlas.incf.org/]

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    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/bhs358

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    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. 2013

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    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. 2012

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Acknowledgements

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.

Author information

Correspondence to Christian Nowke.

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Keywords

  • Visual Inspection
  • Simulated Data
  • Simulation Tool
  • Spike Activity
  • Simulation Technology