Micro-CTvlab: A web based virtual gallery of biological specimens - - PowerPoint PPT Presentation

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Micro-CTvlab: A web based virtual gallery of biological specimens - - PowerPoint PPT Presentation

Dec 06, 2022 265 likes •662 views

Micro-CTvlab: A web based virtual gallery of biological specimens using micro-computed tomography By : Kleoniki Keklikoglou, Eva Chatzinikolaou, Sarah Faulwetter, Irene Filiopoulou, Nikitas Michalakis, Nikos Minadakis, Emmanouela Panteri, George

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Micro-CTvlab: A web based virtual gallery of biological specimens using micro-computed tomography

By: Kleoniki Keklikoglou, Eva Chatzinikolaou, Sarah Faulwetter, Irene Filiopoulou, Nikitas Michalakis, Nikos Minadakis, Emmanouela Panteri, George Perantinos, Daniel DiCorpo, Farah Ahmed, Gordon Patterson, James Michaelson, Christos Arvanitidis

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LifeWatch Greece

What is micro-CT?

  • Non destructive three-dimensional

imaging technique similar to computer tomography used in hospitals, just on a much smaller scale

  • Samples of a few millimeters up to a

size of a mouse, and structures in the range of a few microns (<0,8μm/pixel) can be seen in the images

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What is micro-CT?

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Scanning procedure

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Image acquisition

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Visualisation

Exterior parts Interior parts

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The idea

Source: http://www.naturkundemuseum-berlin.de/typo3temp/pics/d09e9f46e0.jpg

Godfray, HCJ (2007) Linnaeus in the information age. Nature 446: 259–260

Type material Cybertype

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  • provide morphological and anatomical information of the same

accuracy and reliability as the physical type material

A cybertype should...

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  • be linked to the original type material, which can be

consulted if in doubt

A cybertype should...

Bruker Micro-CT User Meeting 2015

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  • be created without affecting the morphological,

anatomical and molecular identity of the physical specimen

Bruker Micro-CT User Meeting 2015

A cybertype should...

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  • be retrievable

A cybertype should... … but how??

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 The development of a virtual micro-CT virtual

laboratory (Micro-CT vLab) aims at making the micro- CT data exploration of natural history specimens freely available over the Internet

 This vLab has been created in the context of the

LifeWatch Research Infrastructure (ESFRI)

Through the way of cybertype creation...

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LifeWatch - the concept of ESFRIs

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LifeWatch - challenges (Questions)

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LifeWatch - challenges (Ifrastructure)

VRE: Virtual Research Environment

  • e-Services (electronic services)
  • vLabs (virtual laboratories)
  • Computational capacity unlimited space
  • Transparency in scientific research practice
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LifeWatchGreece Research (e-)Infrastructure

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But how about if we start the real integration in biology?

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But how about if we start the real integration in biology? Example from IMGs

miro_CT scan phenomics phenome

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Micro-CT virtual galleries

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

  • 650 scans have been created and for the initiation of this web service only 17
  • f them were uploaded
  • The uploaded datasets belong to several marine species and they are fully

annotated with metadata

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Accessed through LifeWatchGreece Portal

portal.lifewatchgreece.eu

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Home Page

Scans are presented as a preview of images with the title of the dataset

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Search tool

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The micro-CT dataset

Short description of the dataset Gallery of 3D images Related datasets

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3D visualization

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3D visualization

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Video

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Metadata

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Mobile App

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Conclusions

A cybertype should…

  • provide morphological and anatomical information of the

same accuracy and reliability as the physical type material Technological progress is still required  Combination with other digitization methods

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A cybertype should…

  • be linked to the original type material, which can be

consulted if in doubt

 Standards for proper curation and documentation of 3D-types

should be developed (by museums and IT community)

Conclusions

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A cybertype should…

  • be created without affecting the morphological, anatomical

and molecular identity of the physical specimen

  •  Experiments (staining – de-staining, genetic etc) concerning a

variety of organisms is still required

Conclusions

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A cybertype should…

  • be retrievable

However...

 Installation of a storage area network (SAN)  Standards for proper curation and documentation of 3D-

types should be developed is a first step

Conclusions

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 In the long term these developments will transform taxonomic

research into a true cyber-discipline

 More and more morphological and anatomical data will become

available in an electronic, shareable format

 This will speed up systematic research, as morphological, high-

resolution information can be accessed at the click of a mouse, and analyzed in completely new ways by 3D pattern recognition algorithms

 Steering comparative morphology into a new direction and

shifting from the current use of phenetics to that of phenomics

Conclusions

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Conclusions

Where are we now? Developing a draft WP for a proposal on Museums and collections (BioUnify; COST instrument (EU))

The overall objective of such a WP would be to: “bring all the scientific community interested in the micro-CT scanning technology for natural sciences and biodiversity together in order to discuss and decide on issues that are required to achieve a consensus on sharing and distributing data and metadata, and the development of the respective infrastructure at the international scale”. Therefore, the specific objectives of such a WP might be:

 Creation of standards of the data files needed to be stored;  Creation of protocols and standards of meta-data;  Storage space solutions;  Development of strategy on the terms of use for data and metadata;  3D pattern recognition technology solutions;  Design and roadmap for the development of an international distributed infrastructure.

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Thank you

https://www.youtube.com/watch?v=RcAjPIZVla0

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