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

Markéta Tesařová,Markéta Kaucká,Jozef Kaiser,Igor Adameyko,Shahragim Tajbakhsh,Eglantine Heude,Tomáš Zikmund,Glenda Comai

doi:10.1038/s41598-019-51180-2

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.

Highlights

To facilitate assimilation and visualisation of microcomputed tomography (microCT) datasets, interactive 3D Portable Document Format (PDF) has been used in different field including in developmental biology[6,19,20], in human physiology and anatomy[4,21,22,23], in entomology[24] and marine biology[25,26]
We provide an alternative, user-friendly way to create interactive 3D PDF files from microCT datasets taking the complexity of mouse craniofacial anatomy as a model example
We present a detailed, user-friendly protocol for the surface rendering of craniofacial structures including soft tissues as well as of hard tissues, with a step-by-step procedure from sample collection to the creation of an interactive 3D PDF

Summary

Introduction

We provide an alternative, user-friendly way to create interactive 3D PDF files from microCT datasets taking the complexity of mouse craniofacial anatomy as a model example. To create an interactive 3D PDF from microCT data, the critical steps are: (i) chemical contrasting of biological samples if soft tissues are to be visualized, (ii) data acquisition and (iii) CT virtual reconstruction (Fig. 1). This is followed by data processing, the most critical step consisting of segmentation, surface extraction, adjustment of segmented 3D models, and conversion into a final interactive PDF file. We provide a detailed description of each step of the pipeline (see Supplementary Material 1)

Methods

Findings

Conclusion