2020/2/22 Hackathon wrap-up - INCF Japan Node · What is Standard 3D viewer and its GUI...

2020/2/22 Hackathon wrap-up

Tomoki Kazawa@CNS-PF committee

cns.neuroinf.jphttps://invbrain.neuroinf.jp/

Two topics about improvement of 3D

3D web viewer

Ontology integration

Two topics about improvement of 3D

3D web viewer

Ontology integration

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

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

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

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

• )

Two topics about improvement of 3D

3D web viewer

Ontology integration

Our database contents

• 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)

• 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