Tutorial Session

November 27(Friday)14:00-15:30

RCAST M2 Room 251


Title: A method for construction and application of standard brain model based on the confocal images


Tutor Hidetoshi IKENO
, School of Human Science and EnvironmentUniversity of Hyogo School

※Advance Registration necessary to AINI2015 Secretaliat e-mail:aini2015[@]nijc.brain.riken.jp



      Tutorial Sesssion Text             Data                           Software

      (PDF 16p Japanese Ver.)          (ZIP file 366MB)         ( ZIP file 1.9GB)



Hidetoshi IKENO1, Daisuke MIYAMOTO2, Tomoki KAZAWA2 and Ryohei KANZAKI2

1University of Hyogo, Himeji, Japan; 2RCAST, The University of Tokyo, Tokyo, Japan


Standardization of data is an important activity for integrating various experimental achievements. The activities to construct the standard brain for various spices could drive forward to reveal brain structures and functions. In this tutorial, we present a general method to construct a standard brain model from the confocal microscope images. The course is conducting following steps;

  1. Constructing the standard brain frame model (SBFM): The standardized outer shape of brain is obtained by averaging of rigid registered individual brain image data. SBFM can be constructed by making object model from the standardized outer shape image.
  2. Registration of brain image into SBFM: The detail image of brain can be registered into the SBFM by using landmarks on the outline of brain as clues for transformation.
  3. Segmentation of neuron from the confocal image data: Neuronal structure is automatically or semi-automatically segmented from confocal images by using some tracing software. SWC format is commonly used for describing neuronal structure model.
  4. Registration of neuron model into the standard brain model: Non-rigid transformation can be effectively used for registration of neuron model into the standard brain. The registration results will be used for analyzing neuronal network connection and communication.

Technique and software presenting in this tutorial can be applied to various species. This session is conducted in Japanese.

    (FIgure TBA)

Figure:  Image data of neuron (A) and landmarks on the standard brain (B). Segmentation result of neuron (C) and registered neuron into the standard brain (D).


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