Three-Dimensional Portable Document Format (3D PDF) in Clinical Communication and Biomedical Sciences: Systematic Review of Applications, Tools, and Protocols

Clinical Applications of Mixed Reality and 3D Printing in Congenital Heart Disease

Understanding the anatomical features and generation of realistic three-dimensional (3D) visualization of congenital heart disease (CHD) is always challenging due to the complexity and wide spectrum of CHD. Emerging technologies, including 3D printing and mixed reality (MR), have the potential to overcome these limitations based on 2D and 3D reconstructions of the standard DICOM (Digital Imaging and Communications in Medicine) images. However, very little research has been conducted with regard to the clinical value of these two novel technologies in CHD. This study aims to investigate the usefulness and clinical value of MR and 3D printing in assisting diagnosis, medical education, pre-operative planning, and intraoperative guidance of CHD surgeries through evaluations from a group of cardiac specialists and physicians. Two cardiac computed tomography angiography scans that demonstrate CHD of different complexities (atrial septal defect and double outlet right ventricle) were selected and converted into 3D-printed heart models (3DPHM) and MR models. Thirty-four cardiac specialists and physicians were recruited. The results showed that the MR models were ranked as the best modality amongst the three, and were significantly better than DICOM images in demonstrating complex CHD lesions (mean difference (MD) = 0.76, p = 0.01), in enhancing depth perception (MD = 1.09, p = 0.00), in portraying spatial relationship between cardiac structures (MD = 1.15, p = 0.00), as a learning tool of the pathology (MD = 0.91, p = 0.00), and in facilitating pre-operative planning (MD = 0.87, p = 0.02). The 3DPHM were ranked as the best modality and significantly better than DICOM images in facilitating communication with patients (MD = 0.99, p = 0.00). In conclusion, both MR models and 3DPHM have their own strengths in different aspects, and they are superior to standard DICOM images in the visualization and management of CHD.

Integrating Data Directly into Publications with Augmented Reality and Web-Based Technologies – Schol-AR

Scientific research has become highly intertwined with digital information, however scientific publication remains based on the static text and figures of principal articles. This discrepancy constrains complex scientific data into 2D static figures, hindering our ability to effectively exchange the complex and extensive information that underlies modern research. Here, we demonstrate how the viewing of digital data can be directly integrated into the existing publication system through both web based and augmented reality (AR) technologies. We additionally provide a framework that makes these capabilities available to the scientific community. Ultimately, augmenting articles with data can modernize scientific communication by bridging the gap between the digital basis of present-day research and the natural limitations of printable articles.

A reverse form of Linburg-Comstock variation with comments on its etiology and demonstration of interactive 3D portable document format

Purpose

Two most common variations of flexor pollicis longus include its accessory head and its connection with the flexor digitorum profundus of the index (Linburg–Comstock variation). In addition, while three-dimensional (3D) screening has widely been used in anatomical education, its use as reporting tool in anatomical research is still limited. The objective of this study is to report a previously unrecognized form of the accessory head of flexor pollicis longus, discuss the potential etiology of Linburg–Comstock variation, and pilot the 3D scanning of a large-scale anatomical structure.

Methods

An unusual tendon slip was discovered during a routine dissection in the anterior compartment of the right forearm of a 54-year-old male cadaver. A 3D scanner was used to capture the surface topography of the specimen and an interactive portable document format (PDF) was created.

Results

An anomalous tendon was found originating from the lateral aspect of the flexor digitorum profundus muscle. This variant tendon then inserted onto the medial surface of the flexor pollicis longus tendon before entering the carpal tunnel. The variation resembles a reverse form of Linburg–Comstock variation, because pulling this variant tendon resulted in simultaneous flexion of the interphalangeal joint of thumb.

Conclusion

Surgeons should be aware of the reverse Linburg–Comstock variation, because it may not be detectable by the conventional provocative testing. Linburg–Comstock variation may be classified as an anatomical variant or a secondarily acquired condition depending on its type. Our demonstration of interactive 3D-PDF file highlights its potential use for delivering anatomical information in future cadaveric studies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00276-021-02858-8.

Embedding interactive, three-dimensional content in portable document format to deliver gross anatomy information and knowledge

The Portable Document Format (PDF) is likely the most widely used digital file format for scholarly and scientific electronic publishing. Since format specification version 1.6, three-dimensional (3D) models in Universal 3D (U3D) format can be embedded into PDF files. The present study demonstrates a repertoire of graphic strategies and modes of presentation that exploit the potentials of 3D models embedded in PDF to deliver anatomical information and knowledge. Three-dimensional models and scenes representing anatomical structures generated by 3D surface scanning or by segmentation from either clinical imaging data or cadaver sectional images were converted into U3D format and then embedded into PDF files using both freely and commercially available software. The relevant steps and required software tools are described. Built-in tools in Adobe Acrobat and JavaScript scripting both were used to pre-configure user interaction with 3D contents. Eight successive proof-of-concept examples of increasing complexity are presented and provided as supplementary material, including both unannotated and annotated 3D specimens, use of bitmap-textures, guided navigation through predetermined 3D scenes, 3D animation, and interactive navigation through tri-planar sectional human cadaver images. Three-dimensional contents embedded in PDF files are generally comparable to multimedia and dedicated 3D software in terms of quality, flexibility, and convenience, and offer new unprecedented opportunities to deliver anatomical information and knowledge.

Technical Protocol for Presenting Maxillofacial Prosthetics Concepts to Dental Students using Interactive 3D Virtual Models within a Portable Document Format

An appropriate presentation of maxillofacial defects and their prosthetic rehabilitation concepts using traditional two-dimensional educational materials is challenging for dental students and prosthodontics residents. This technique article introduces a simple approach to visualize and communicate three-dimensional (3D) virtual models embedded into a portable document format (PDF) file for presenting maxillofacial prosthetics concepts and enhancing students' spatial ability when learning maxillofacial prosthetics. MeVisLab software was used to combine various maxillofacial models and save them as a single 3D model. Adobe Acrobat Pro DC software was used to import the 3D model and create interactive visualization PDF documents. Adobe reader software was then used to visualize the content of the PDF documents. This approach allows educators to develop PDF files with multiple 3D models for teaching maxillofacial prosthetics concepts and communicate them with their students. Students can simply open the PDF file, activate the 3D mode, and interactively manipulate the 3D models to enhance their spatial ability for learning maxillofacial prosthetics.

A comprehensive and user-friendly framework for 3D-data visualisation in invertebrates and other organisms

Methods for 3D‐imaging of biological samples are experiencing unprecedented development, with tools such as X‐ray micro‐computed tomography (μCT) becoming more accessible to biologists. These techniques are inherently suited to small subjects and can simultaneously image both external and internal morphology, thus offering considerable benefits for invertebrate research. However, methods for visualising 3D‐data are trailing behind the development of tools for generating such data. Our aim in this article is to make the processing, visualisation and presentation of 3D‐data easier, thereby encouraging more researchers to utilise 3D‐imaging. Here, we present a comprehensive workflow for manipulating and visualising 3D‐data, including basic and advanced options for producing images, videos and interactive 3D‐PDFs, from both volume and surface‐mesh renderings. We discuss the importance of visualisation for quantitative analysis of invertebrate morphology from 3D‐data, and provide example figures illustrating the different options for generating 3D‐figures for publication. As more biology journals adopt 3D‐PDFs as a standard option, research on microscopic invertebrates and other organisms can be presented in high‐resolution 3D‐figures, enhancing the way we communicate science.

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

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.