MicroCT is a component of the LifewatchGreece Infrastructure, which is currently under development within the context of the LifeWatch ESFRI Project.

1. 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

2. 24/23/2015
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/ .
LifeWatch Greece

3. 34/23/2015
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.
LifeWatch Greece

4. 44/23/2015
LifeWatchGreece
portal.lifewatchgreece.eu
Accessed by the LifeWatchGreece Portal

5. 54/23/2015
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

6. 64/23/2015
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.
LifeWatch Greece

7. 74/23/2015
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
LifeWatch Greece

8. 84/23/2015
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.
LifeWatch Greece

9. 94/23/2015
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.
LifeWatch Greece

10. 104/23/2015
Video
● By clicking “Video” tab
one or more videos
created for this specimen
in the microCT can be
viewed.
LifeWatch Greece

11. 114/23/2015
Metadata Catalogue
● The “Metadata Catalogue”
tab leads to many useful
data/metadata about the
specimen.
LifeWatch Greece

12. 124/23/2015
Mobile application: MicroCT
LifeWatchGreece
portal.lifewatchgreece.eu
LifeWatch Greece
Click the microCT Button

13. 134/23/2015
MicroCt Mobile app workflow
LifeWatch Greece
MicroCT mobile application

14. 144/23/2015
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 ;)