Special session

November 27(Friday)9:30-10:50



Collaborative Tool developments at INCF Japan Node Hackathon toward Digital Brain Atlas


Organizer   Tomoki  KAZAWA    Research Center for Advanced Science and Technology (RCAST), The University of Tokyo


                  Session Abstract



In this session we will show J node activities about the developments of the software tools that handle brain images on our database platforms which have begun this year in relation to the Brain Atlas Ideathon/Hackathon 2015 (BAH2015).

INCJ Japan node is running more than 12 database platforms to preserve and open vast neuroscience data in japan.  However, it is importance not only to share the data on database in scientific and general communities but analyse and integrate these data systematically on databases. This year we focused (3D) images of neuron or brain which are typical large size brain data one important axis of the integration. BHA2015 were organized as a kick-start event for facilitating information exchange and collaborative software development for the data integration via brain image data. More than 20 people gathered ideathon (7/16, Riken) and developed software tools for three-day hackathon (9/5-7, Riken). The contents in the ideation and hackathon is open in www page (/bah2015/ideathon.html).

This session mimics ideathon hackathon structures in BAH2015. In the first half two speaker Dr Matsuda and Dr Alexander will speak about their 3D brain image data tools, Brain explorer and 3D slicer. In the latter half five group leaders will talk about achievement in the BAH 2015 and after that.



Session Program       


Part1 Fundamental softwares for brain atlas

Brain   Image Registration Using the ANTs Normalization Toolkit    

Alexander WOODWARD, Neuroinformatics Japan Center, RIKEN Brain Science Institute

Web-based Application to Visualize 3D Brain Atlas    



Part2 Hackathon development

Development of protocol and software for registration in situ hybridization image into the standard brain    

Hidetoshi IKENO, University of Hyogo


Recording the Analyses single neuron morphology on database     

Tomoki KAZAWA, The University of Tokyo


Brain Atlas Hackathon 2015: Pipeline Development for Brain Atlas Registration using The IPython Notebook Computational Environment     

Alexander WOODWARD, Neuroinformatics Japan Center, RIKEN Brain Science Institute


Preprocessing the confocal microscopy images for Neuron Segmentation    

Tetsuya FUKUDA, Graduate School of Information Science and Technology, The University of Tokyo


Improvement of a Web-based Application for 3D Brain Atlas Visualization    



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