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

M. Tesařová, E. Heude, G. Comai, T. Zikmund, M. Kaucká, I. Adameyko, S. Tajbakhsh, J. Kaiser,

. 2019 ; 9 (1) : 14896. [pub] 20191017

Jazyk angličtina Země Velká Británie

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc20028789

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.

Citace poskytuje Crossref.org

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$a 3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.
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$a Heude, Eglantine $u Department Adaptation du Vivant, Museum national d'Histoire naturelle, CNRS UMR 7221, Paris, France. Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France. CNRS UMR, 3738, Paris, France.
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$a Zikmund, Tomáš $u Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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$a Kaucká, Markéta $u Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden. Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria.
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$a Adameyko, Igor $u Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden. Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria.
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$a Tajbakhsh, Shahragim $u Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France. CNRS UMR, 3738, Paris, France.
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$a Kaiser, Jozef $u Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic. kaiser@fme.vutbr.cz.
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