Dataset Information

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

ABSTRACT: 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.

SUBMITTER: Newe A

PROVIDER: S-EPMC3829830 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Publications

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

Newe Axel A Ganslandt Thomas T

PloS one 20131115 11

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 biome ...[more]

PMID: 24260144

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Project description: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.

Project description:ObjectiveThe extent to which biomedical authors have received training in publication ethics, and their attitudes and opinions about the ethical aspects of specific behaviours, have been understudied. We sought to characterise the knowledge and attitudes of biomedical authors about common issues in publication ethics.DesignCross-sectional online survey.Setting and participantsCorresponding authors of research submissions to 20 journals.Main outcome measuresPerceived level of unethical behaviour (rated 0 to 10) presented in five vignettes containing key variables that were experimentally manipulated on entry to the survey and perceived level of knowledge of seven ethical topics related to publishing (prior publication, author omission, self-plagiarism, honorary authorship, conflicts of interest, image manipulation and plagiarism).Results4043/10 582 (38%) researchers responded. Respondents worked in 100 countries and reported varying levels of publishing experience. 67% (n=2700) had received some publication ethics training from a mentor, 41% (n=1677) a partial course, 28% (n=1130) a full course and 55% (n=2206) an online course; only a small proportion rated training received as excellent. There was a full range (0 to 10 points) in ratings of the extent of unethical behaviour within each vignette, illustrating a broad range of opinion about the ethical acceptability of the behaviours evaluated, but these opinions were little altered by the context in which it occurred. Participants reported substantial variability in their perceived knowledge of seven publication ethics topics; one-third perceived their knowledge to be less than 'some knowledge' for the sum of the seven ethical topics and only 9% perceived 'substantial knowledge' of all topics.ConclusionsWe found a large degree of variability in espoused training and perceived knowledge, and variability in views about how ethical or unethical scenarios were. Ethical standards need to be better articulated and taught to improve consistency of training across institutions and countries.

Dataset Information

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

Publications

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

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