lifewatch greece web and mobile application for the microct
TRANSCRIPT
14/23/2015
by Emmanouela Panteri
Contributors: Kleoniki Keklikoglou, Sarah Faulwetter, Nikitas Michalakis, Irene Filiopoulou, Emmanouela Panteri, Nikos Minadakis, George Perantinos, Christos Arvanitidis
LifeWatch Greece web and mobile application for the MicroCT
EGI Lifewatch CC, September 2 2015 Santander
LifeWatch Greece
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MicroCT Tomograph Virtual Galleries
● Micro Computed Tomography ● MicroCT is a non-destructive X-ray imaging technique
which allows the rapid creation of high-resolution three-dimensional data
● MicroCT offers the option to visualise the exterior and the interior parts of an object
● MicroCT services are now available through http://microct.portal.lifewatchgreece.eu/ .
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Micro-CT Tomograph Virtual Galleries
● Furthermore, 7 micro-CT datasets can be downloaded from the Dryad Digital Repository which is a repository system for several datatypes.
● The remaining datasets can be shared through personal communication as the storage is still under construction.
● More than 650 scans have been created in total and for the initiation of this web service only 17 of them were uploaded.
● The uploaded datasets come from several marine organisms and they are fully annotated with metadata.
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portal.lifewatchgreece.eu
Accessed by the LifeWatchGreece Portal
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The MicroCT
LifeWatch Greece
● This virtual lab allows the user to observe a series of images and videos of the datasets
● In the main page, scans are presented as a preview of images with the title of the dataset
● Specifically, these 17 datasets refer to several marine organisms scanned by different parameters.
Main Page
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The MicroCT
● By clicking a dataset, a page with the specimen’s details is revealed.
● The classification of the specimen with a summary of the micro-CT dataset are presented.
● The user can see a series of 3D images of the specimen and other micro-CT related datasets
● Three more tabs are designed which allow the user to manipulate the 3D dataset.
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Slice:Drop
● This virtual lab allows the user to manipulate the 3D models through the non-commercial web-based software Slice:Drop (http://slicedrop.com/).
● Slice:Drop is a web-based 2D/3D viewer using WebGL and HTML5 Canvas to perform image rendering in a web browser.
● Based on the open source XTK toolkit, Slice:Drop runs on computers and mobile devices.
Slicedrop main page
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Nifty files @ Slice:Drop
● By clicking “Nifti” tab there is a window which shows the micro-CT dataset in 3 orthogonal views (x, y, z axes).
● Scrolling the image zooms in and out.
● Left clicking rotates the specimen.
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Nifty files @ Slice:Drop
● Moving the colored cursors the different slices of the dataset can be observed.
● By clicking the small squares in the volume tab, the specimen can be paint and contrasts with the different colors are created.
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Video
● By clicking “Video” tab one or more videos created for this specimen in the microCT can be viewed.
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Metadata Catalogue
● The “Metadata Catalogue”
tab leads to many useful
data/metadata about the
specimen.
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Mobile application: MicroCT
LifeWatchGreece
portal.lifewatchgreece.eu
LifeWatch Greece
Click the microCT Button
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MicroCt Mobile app workflow
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MicroCT mobile application
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LifeWatchGreece
LifeWatchGreece Research Infrastructure , funded by the GSRT (Greek government: structural funds), is the national effort to address the above requirement and to support relevant studies.To materialize its aim, LWG RI adheres to the central lifewatch.eu guidelines, and attempts to ally all the Greek scientific human resources working on biodiversity data and data observatories.Coordinated by the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC, www.imbbc.hcmr.gr) of the Hellenic Center for Marine Research (HCMR, www.hcmr.gr), LWG includes 49 partner institutions covering a wide range of scientific disciplines (terrestrial, marine and freshwater biology, zoology, botany, geography, forestry, agriculture, genetics, biotechnology, pharmacy, aquaculture, education and law).
LifeWatch Greece
Thank you ;)