2020/2/22 hackathon wrap-up - incf japan node · what is standard 3d viewer and its gui...
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2020/2/22 Hackathon wrap-up
Tomoki Kazawa@CNS-PF committee
cns.neuroinf.jphttps://invbrain.neuroinf.jp/
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Two topics about improvement of 3D
3D web viewer
Ontology integration
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Two topics about improvement of 3D
3D web viewer
Ontology integration
![Page 4: 2020/2/22 Hackathon wrap-up - INCF Japan Node · What is Standard 3D viewer and its GUI manipulations ? •Survey of Standard 3D view •Yokota G • Blender • Meshlab •WE use](https://reader035.vdocuments.mx/reader035/viewer/2022062607/60574616d15d097cbb2fcabb/html5/thumbnails/4.jpg)
What is Standard 3D viewer and its GUI manipulations ?
• Survey of Standard 3D view
• Yokota G• Blender• Meshlab
• WE use ParaviewAmira/AvizoneuTube
Web based
From OkumuraRii-mango/Papayahttp://api.goxtk.com/
We build X3d dom 3D viewer
From TanakaThree.jshttps://aframe.io/
Paraview mouse manipulation (surveyed by Sakai)
http://www.mech.iwate-u.ac.jp/~hirose/ockitatohoku/ref/nakayamasama-paraview.pdf
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Our 3D viewer
https://cns.neuroinf.jp/modules/pico/index.php?content_id=11&ml_lang=en
https://cns.neuroinf.jp/modules/pico/index.php?content_id=12
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https://cns.neuroinf.jp/modules/pico/index.php?content_id=11&ml_lang=en
https://cns.neuroinf.jp/modules/pico/index.php?content_id=12
https://cns.neuroinf.jp/x3d/show_cns.php?file_id=18010&fullscreen=1
BugbFix byOkumura 2/21
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Plan
• GUI and key binding will be modified to a faily common interface.
• View from Infinity distance
• Scale bard
• Viewer for two objects each volume scale is extremely different ( ex. insect and wheel
• )
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Two topics about improvement of 3D
3D web viewer
Ontology integration
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Our database contents
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• My plan• Integrate meta data and the information in the document using
Semantic media wiki and intoroducing some OWLs (species and anatomy)
• What I did• Build a server in LAN (centos7.6 Apache 2.4 mySQL5.7 Media wiki
1.34)• A trouble with Composer (PHP) prevent to build Semantic media
wiki 1.33)
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• Drosophila Anatomy Ontology (DAO)in mainteined as Drosophila anatomy and development ontologies
• https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/wiki
• Parts of Table S1. Neuropil supercategories (level 1) were used
•
• OL optic lobe
• MB mushroom body
• CX central complex
• LX lateral complex
• VLNP ventrolateral neuropils
• LH lateral horn
• SNP superior neuropils
• INP inferior neuropils
• AL antennal lobe
• VMNP ventromedial neuropils
• PENP periesophageal neuropils
• GNG gnathal ganglia
Existing databases in IVB-PF
Make link and keyword pages in mediawikiMaking categories
Wiki for metadata integration
Previous work: Most of data descricption and keyword information were copied into media-wiki
Our data with meta metadatas