3D Portable Document Format Research Articles

Investigation of the Clinical Value of Four Visualization Modalities for Congenital Heart Disease.

Diagnosing congenital heart disease (CHD) remains challenging because of its complex morphology. Representing the intricate structures of CHD on conventional two-dimensional flat screens is difficult owing to wide variations in the pathologies. Technological advancements, such as three-dimensional-printed heart models (3DPHMs) and virtual reality (VR), could potentially address the limitations of viewing complex structures using conventional methods. This study aimed to investigate the usefulness and clinical value of four visualization modalities across three different cases of CHD, including ventricular septal defect, double-outlet right ventricle, and tetralogy of Fallot. Seventeen cardiac specialists were invited to participate in this study, which was aimed at assessing the usefulness and clinical value of four visualization modalities, namely, digital imaging and communications in medicine (DICOM) images, 3DPHM, VR, and 3D portable document format (PDF). Out of these modalities, 76.4% of the specialists ranked VR as the best for understanding the spatial associations between cardiac structures and for presurgical planning. Meanwhile, 94.1% ranked 3DPHM as the best modality for communicating with patients and their families. Of the various visualization modalities, VR was the best tool for assessing anatomical locations and vessels, comprehending the spatial relationships between cardiac structures, and presurgical planning. The 3DPHM models were the best tool for medical education as well as communication. In summary, both 3DPHM and VR have their own advantages and outperform the other two modalities, i.e., DICOM images and 3D PDF, in terms of visualizing and managing CHD.

3D Documentation with TLS of Caliphal Gate (Ceuta, Spain)

Three-dimensional surveying with a terrestrial laser scanner (TLS) has implied a revolution in the field of 3D modeling, as this methodology provides detailed point-clouds with simplified processes of capture. In addition to the point-clouds, other outputs can be obtained, such as ortho-images, virtual itineraries, 2D cartography, and meshes, which implies a second avenue of multimedia products, such as 3D Portable Document Format (PDF) files and interactive applications. All these options are interesting for the management and broadcast of cultural heritage. The works that have been developed in this research are aimed at setting a workflow for the TLS surveying works and subsequent data management for the generation of a 3D model of the Caliphal Gate of Ceuta, which is considered as one of the most important medieval findings in Spain in recent years, and its immediate surroundings. This model and the different outputs that have been obtained from it allow for the continuation of the historiographic analysis of the complex, while documenting a partial stage in the development of the works of enhancement. In addition to this, these products are not only useful in terms of conservation studies or enhancement, as they are also suitable for the dissemination of the site. Special attention has been set on the paid suitable software for data management while generating the outputs, and for its application by the final users.

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.

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

BackgroundThe Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians.ObjectiveThe objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology.MethodsA systematic literature review was performed using PubMed and Google Scholar. Articles searched for were in English, peer-reviewed with biomedical reference, published since 2005 in a journal or presented at a conference or scientific meeting. Ineligible articles were removed after screening. The found literature was categorized into articles that (1) applied 3D PDF for visualization, (2) showed ways to use 3D PDF, and (3) provided tools or protocols for the creation of 3D PDFs or necessary models. Finally, the latter category was analyzed in detail to provide an overview of the state of the art.ResultsThe search retrieved a total of 902 items. Screening identified 200 in-scope publications, 13 covering the use of 3D PDF for medical purposes. Only one article described a clinical routine use case; all others were pure research articles. The disciplines that were covered beside medicine were many. In most cases, either animal or human anatomies were visualized. A method, protocol, software, library, or other tool for the creation of 3D PDFs or model files was described in 19 articles. Most of these tools required advanced programming skills and/or the installation of further software packages. Only one software application presented an all-in-one solution with a graphical user interface.ConclusionsThe use of 3D PDF for visualization purposes in clinical communication and in biomedical publications is still not in common use, although both the necessary technique and suitable tools are available, and there are many arguments in favor of this technique. The potential of 3D PDF usage should be disseminated in the clinical and biomedical community. Furthermore, easy-to-use, standalone, and free-of-charge software tools for the creation of 3D PDFs should be developed.

A Novel and Freely Available Interactive 3d Model of the Internal Carotid Artery.

We describe a new and freely available 3D interactive model of the intracranial internal carotid artery (ICA) and the skull base that also allows to display and compare its main segment classifications. High-resolution 3D human angiography (isometric voxel's size 0.36mm) and Computed Tomography angiography images were exported to Virtual Reality Modeling Language (VRML) format for processing in a 3D software platform and embedding in a 3D Portable Document Format (PDF) document that can be freely downloaded at http://diposit.ub.edu/dspace/handle/2445/112442 and runs under Acrobat Reader on Mac and Windows computers and Windows 10 tablets. The 3D-PDF allows for visualisation and interaction through JavaScript-based functions (including zoom, rotation, selective visualization and transparentation of structures or a predefined sequence view of the main segment classifications if desired). The ICA and its main branches and loops, the Gasserian ganglion, the petrolingual ligament and the proximal and distal dural rings within the skull base environment (anterior and posterior clinoid processes, silla turcica, ethmoid and sphenoid bones, orbital fossae) may be visualized from different perspectives. This interactive 3D-PDF provides virtual views of the ICA and becomes an innovative tool to improve the understanding of the neuroanatomy of the ICA and surrounding structures.

Enriching scientific publications with interactive 3D PDF: an integrated toolbox for creating ready-to-publish figures

Three-dimensional (3D) data of many kinds is produced at an increasing rate throughout all scientific disciplines. The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents and allows for embedding three-dimensional models. Therefore, it is a well-suited medium for the visualization and the publication of this kind of data. The generation of the appropriate files has been cumbersome so far. This article presents the first release of a software toolbox which integrates the complete workflow for generating 3D model files and ready-to-publish 3D PDF documents for scholarly publications in a consolidated working environment. It can be used out-of-the-box as a simple working tool or as a basis for specifically tailored solutions. A comprehensive documentation, an example project and a project wizard facilitate the customization. It is available royalty-free and for Windows, MacOS and Linux.

Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files.

The Portable Document Format (PDF) allows for embedding three-dimensional (3D) models and is therefore particularly suitable to communicate respective data, especially as regards scholarly articles. The generation of the necessary model data, however, is still challenging, especially for inexperienced users. This prevents an unrestrained proliferation of 3D PDF usage in scholarly communication. This article introduces a new solution for the creation of three of types of 3D geometry (point clouds, polylines and triangle meshes), that is based on MeVisLab, a framework for biomedical image processing. This solution enables even novice users to generate the model data files without requiring programming skills and without the need for an intensive training by simply using it as a conversion tool. Advanced users can benefit from the full capability of MeVisLab to generate and export the model data as part of an overall processing chain. Although MeVisLab is primarily designed for handling biomedical image data, the new module is not restricted to this domain. It can be used for all scientific disciplines.

Application and Evaluation of Interactive 3D PDF for Presenting and Sharing Planning Results for Liver Surgery in Clinical Routine

Background & ObjectivesThe Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents. It is platform-independent, suitable for the exchange of medical data, and allows for the embedding of three-dimensional (3D) surface mesh models. In this article, we present the first clinical routine application of interactive 3D surface mesh models which have been integrated into PDF files for the presentation and the exchange of Computer Assisted Surgery Planning (CASP) results in liver surgery. We aimed to prove the feasibility of applying 3D PDF in medical reporting and investigated the user experience with this new technology.MethodsWe developed an interactive 3D PDF report document format and implemented a software tool to create these reports automatically. After more than 1000 liver CASP cases that have been reported in clinical routine using our 3D PDF report, an international user survey was carried out online to evaluate the user experience.ResultsOur solution enables the user to interactively explore the anatomical configuration and to have different analyses and various resection proposals displayed within a 3D PDF document covering only a single page that acts more like a software application than like a typical PDF file (“PDF App”). The new 3D PDF report offers many advantages over the previous solutions. According to the results of the online survey, the users have assessed the pragmatic quality (functionality, usability, perspicuity, efficiency) as well as the hedonic quality (attractiveness, novelty) very positively.ConclusionThe usage of 3D PDF for reporting and sharing CASP results is feasible and well accepted by the target audience. Using interactive PDF with embedded 3D models is an enabler for presenting and exchanging complex medical information in an easy and platform-independent way. Medical staff as well as patients can benefit from the possibilities provided by 3D PDF. Our results open the door for a wider use of this new technology, since the basic idea can and should be applied for many medical disciplines and use cases.

3D interactive model of lumbar spinal structures of anesthetic interest.

A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information.

Simplified Generation of Biomedical 3D Surface Model Data for Embedding into 3D Portable Document Format (PDF) Files for Publication and Education

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D – it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.

Palaeontology in the third dimension: a comprehensive guide for the integration of three-dimensional content in publications

During the last decade, three-dimensional, digital models have become increasingly important in geosciences and in particular in palaeontological research. Although significant advances in hard- and software technology have facilitated the acquisition and creation of such models, the presentation of three-dimensional data is still greatly handicapped by the traditionally two-dimensional means of publication. The ability to integrate three-dimensional (3D) models, which can be interactively manipulated, into portable document format (PDF) documents not only considerably improves their accessibility, but also represents an innovative, but so far neglected, approach for the presentation and communication of digital data. This article introduces and illustrates a comprehensive workflow for the creation of 3D PDFs, incorporating different techniques and methodological steps, and using both commercial and freely available software resources. Advantages and disadvantages of each method are discussed, and are accompanied by selected examples of digital models. These examples encompass different methods of data acquisition (computed tomography, synchrotron radiation X-ray tomographic microscopy, photogrammetry) and span a wide range of sizes and taxonomic groups. To the best of the author’s knowledge, this article represents the first application of 3D PDF technology fully integrated into a scientific publication in palaeontology or even geosciences, and not restricted to supplementary material. It provides the reader with extended visual information and facilitates the dissemination of data. As both authors and readers benefit greatly from their usage, it is argued that 3D PDFs should become an accepted standard in palaeontological publications of three-dimensional models.

Leaving the structural ivory tower, assisted by interactive 3D PDF

The ability to embed interactive three-dimensional (3D) models into electronic publications in portable document format (PDF) greatly enhances the accessibility of molecular structures. Here, we report advances in this procedure and discuss what is needed to develop this format into a truly useful tool for the structural biology community as well as for readers who are less well trained in molecular visualization.