Pablo de Heras Ciechomski, Robin Mange


This paper presents a method for real-time rendering of a neocortical column in the mouse brain with 10000 individually simulated neurons, as implemented in the software GabrielStudio (TM). It also presents how the same system is used to create movie sequences of scripted camera keyframes for high resolution outputs. The current system is running on an SGI Altix Prism Extreme with 16 parallel graphics cards and a shared memory of 300 GB. Gabrielstudio works as a virtual microscope for computational neuroscientists to analyze their simulations of neurons.


  1. Al-Kofahi, K. A., Lasek, S., Szarowski, D. H., Pace, C. J., Nagy, G., Turner, J. N., and Roysam, B. (2002). Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Transactions on Information Technology in Biomedicine, 6(2):171-187.
  2. BlueBrain (2007). A comoputational neuroscience project at ecole polytechnique federal de lausanne (epfl), lausanne, switzerland.
  3. Can, A., Turner, J., Tanenbaum, H., and Roysam, B. (1999). Rapid automated tracing and feature extraction from live high-resolution retinal fundus images using direct exploratory algorithms.
  4. Carnevale, N. T. and Hines, M. L. (2006). The NEURON Book. Cambridge University Press, New York, NY, USA.
  5. Gumhold, S., Borodin, P., and Klein, R. (2003). Intersection free simplification. International Journal of Shape Modeling (IJSM), 9(2):155-176.
  6. Hill, S. L. and Tononi, G. (2004). Modeling sleep and wakefulness in the thalamocortical system. Journal of Neurophysiology, pages 1671-1698.
  7. Holm, A., Offen, L., and Fellner, D. (2005). Biobrowser a framework for fast protein visualization. In EUROVIS 2005 / IEEE VGTC Symposium on Visualization 2005, pages 287-294.
  8. Kuss, A., Hege, H.-C., Krofczik, S., and Borner, J. (2007). Pipeline for the creation of surface-based averaged brain atlases. accepted for publication.
  9. Luebke, D., Watson, B., Cohen, J. D., Reddy, M., and Varshney, A. (2002). Level of Detail for 3D Graphics. Elsevier Science Inc., New York, NY, USA.
  10. Melek, Z., Mayerich, D., Yuksel, C., and Keyser, J. (2006). Visualization of fibrous and thread-like data. IEEE Transactions on Visualization and Computer Graphics, 12(5):1165-1172.
  11. Schaufler, G. and Stürzlinger, W. (1995). Generating multiple levels of detail from polygonal geometry models. In Göbel, M., editor, Virtual Environments 7895 (Eurographics Workshop), pages 33-41. Springer-Verlag: Heidelberg, Germany.
  12. Stoll, C., Gumhold, S., and Seidel, H.-P. (2005). Visualization with stylized line primitives. In IEEE Visualization, page 88.
  13. Tarini, M., Cignoni, P., and Montani, C. (2006). Ambient occlusion and edge cueing to enhance real time molecular visualization. IEEE Transaction on Visualization and Computer Graphics, 12(6).
  14. Westerhoff, M. (2003). Efficient visualization and reconstruction of 3d geometric models from neurobiological confocal microscope scans. Phd Thesis.

Paper Citation

in Harvard Style

de Heras Ciechomski P. and Mange R. (2008). REALTIME NEOCORTICAL COLUMN VISUALIZATION . In Proceedings of the First International Conference on Bio-inspired Systems and Signal Processing - Volume 2: BIOSIGNALS, (BIOSTEC 2008) ISBN 978-989-8111-18-0, pages 283-288. DOI: 10.5220/0001068102830288

in Bibtex Style

author={Pablo de Heras Ciechomski and Robin Mange},
booktitle={Proceedings of the First International Conference on Bio-inspired Systems and Signal Processing - Volume 2: BIOSIGNALS, (BIOSTEC 2008)},

in EndNote Style

JO - Proceedings of the First International Conference on Bio-inspired Systems and Signal Processing - Volume 2: BIOSIGNALS, (BIOSTEC 2008)
SN - 978-989-8111-18-0
AU - de Heras Ciechomski P.
AU - Mange R.
PY - 2008
SP - 283
EP - 288
DO - 10.5220/0001068102830288