Publication detail

An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format

TESAŘOVÁ, M. HEUDE, E. COMAI, G. ZIKMUND, T. KAUCKÁ, M. ADAMEYKO, I. TAJBAKHSH, S. KAISER, J.

Original Title

An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format

Type

journal article in Web of Science

Language

English

Original Abstract

3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.

Keywords

CT, imaging, 3D, Portable Document Format, 3D PDF

Authors

TESAŘOVÁ, M.; HEUDE, E.; COMAI, G.; ZIKMUND, T.; KAUCKÁ, M.; ADAMEYKO, I.; TAJBAKHSH, S.; KAISER, J.

Released

17. 10. 2019

Publisher

Springer Nature

ISBN

2045-2322

Periodical

Scientific Reports

Year of study

2019

Number

9

State

United Kingdom of Great Britain and Northern Ireland

Pages from

1

Pages to

8

Pages count

8

URL

https://www.nature.com/articles/s41598-019-51180-2#article-info

Full text in the Digital Library

http://hdl.handle.net/11012/181090

BibTex

@article{BUT159285,
  author="Markéta {Kaiser} and Eglantine {Heude} and Glenda {Comai} and Tomáš {Zikmund} and Markéta {Kaucká} and Igor {Adameyko} and Shahragim {Tajbakhsh} and Jozef {Kaiser}",
  title="An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format",
  journal="Scientific Reports",
  year="2019",
  volume="2019",
  number="9",
  pages="1--8",
  doi="10.1038/s41598-019-51180-2",
  issn="2045-2322",
  url="https://www.nature.com/articles/s41598-019-51180-2#article-info"
}