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Toward collaboration in NIJC platforms: Standard brain database linked with application server

Hidetoshi Ikeno1*, Tomoki Kazawa2, Ryohei Kanzaki2, Yoshihiro Okumura3, Yoko Yamaguchi3 and Shiro Usui4
  • 1 University of Hyogo, Sch. Hum. Sci. Env., Japan
  • 2 The University of Tokyo, RCAST, Japan
  • 3 RIKEN BSI, NIJC, Japan
  • 4 Toyohashi University of Technology, EIIRIS, Japan

We are developing and running a platform, Invertebrate Brain Platform (IVB-PF), to provide various research resources, such as neuronal images, behavioral movies and textbook for comparative studies on sensory processing and behavioral control of invertebrates. In the case of silkworm moth, more than 1,000 neuronal image data have been collected and registered. The standard brain image of moth brain has been created and provided (Ikeno et al., 2012). The morphological models of several neurons have been reconstructed and registered in the standard brain. These are provided as contents of our database in stack images, Wavefront OBJ and SWC formats. It is suitable to provide resources as model file for both provider (experimentalist) and user (modeler), because experimentalists can keep original experimental data in their side even register on the platform and users can immediately apply neuron structure on their model simulation by download from the platform.

We are also providing a virtual machine environment with standard application software, such as Fiji, Neuron and Genesis, in neuroscience research through another platform, Simulation Platform (Sim-PF) (Yamazaki et al., 2011). The platform does not only equip utilities for visualization and simulation, but also the high-speed access to the registered data for retrieving and using large amount of data (Fig.1). As the data viewing and applications on the Sim-PF is accessed by user demands from IVB-PF seamlessly, we provide following operations on the registrations and utilizations of the standard brain by the collaboration of these two platforms.
1. Three-dimensional viewing of confocal laser scanning microscope (CLSM) images of the brain and neurons
2. Three-dimensional viewing of standard brain image from various directions
3. Segmentation and modeling of neuropiles and neuron morphologies from CLSM image
4. Registration of neuropiles and neurons into the standard brain
5. Statistical analysis of neuron morphology

To integrate morphological data of a species and compare with others, the standard brain could be a highly effective tool. It is possible to estimate projection regions and synaptic connectivity of neurons. By collaboration of our platforms, we can provide an environment to use neuron morphological data for construction and application of the standard brain. The process and software using on the platform can be applied to various kinds of insect and invertebrate brains.

Figure 1
Image

References

１） H. Ikeno, T. Kazawa, S. Namiki, D. Miyamoto, Y. Sato, S. S. Haupt, I. Nishikawa, R. Kanzaki, Development of a scheme and tools to construct a standard moth brain for neural network simulations, Computational intelligence and neuroscience, 2012, DOI: 10.1155/2012/795291 (2012).
２） T. Yamazaki, H. Ikeno, Y. Okumura, S. Satoh, Y. Kamiyama, Y. Hirata, K. Inagaki, A. Ishihara, T. Kannon, S. Usui, Simulation Platform: A cloud-based online simulation environment. Neural Networks 24(7): 693-698 (2011).

Keywords: standard brain, Silkworm moth, virtual machine, neuron morphology, Neural Stimulation

Conference: Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.

Presentation Type: Poster

Topic: Infrastructural and portal services

Citation: Ikeno H, Kazawa T, Kanzaki R, Okumura Y, Yamaguchi Y and Usui S (2013). Toward collaboration in NIJC platforms: Standard brain database linked with application server. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00109

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Received: 08 Apr 2013; Published Online: 11 Jul 2013.

* Correspondence: Prof. Hidetoshi Ikeno, University of Hyogo, Sch. Hum. Sci. Env., Himeji, Japan, ikeno@shse.u-hyogo.ac.jp