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:BackgroundWe previously demonstrated that in a Japanese national university's medical faculty, overall paper publication frequency increased between 1979-1980 and 2017-2018, while original paper publication did not increase. Further, publication language changed from predominantly Japanese to English. However, whether these trends are specific to medicine or representative of other faculties remains unclear.MethodsWe diachronically analyzed annual university library-produced publication reports for four pharmaceutical and three medical units between 1979-1980 and 2019-2020, elucidating how publication frequency, type, and language medium changed.ResultsAll publication types increased for the pharmaceutical faculty, from 2.87 per faculty member per year to 10.77. Publication of original papers more than doubled, from 1.06 per faculty member per year to 2.37. This increase was exclusively in English publication, with no publication of Japanese original papers in 2019-2020. This contrasts with medicine, which, while it demonstrated similar increases in all publication types combined, from 4.92 papers per faculty member per year to 12.78, did not demonstrate as striking an increase in total original paper publication (English and Japanese), from 1.21 papers per faculty member per year to 1.30. However, these two faculties observed similar trends in that English largely replaced Japanese original paper publication. That both faculties' Japanese original paper publication decreased suggests English language original paper publication comes at the expense of publishing in Japanese. Concerning both faculties together, the increase in publishing frequency for all publication types more than tripled from 4.01 to 12.38. This was largely driven by changes in conference paper publication for the pharmaceutical sciences faculty, where English publication increased 2,775% (0.06 to 1.7 papers per faculty member per year) and Japanese language publication 258% (1.33 to 4.77). While conference paper publication did increase for the medical sciences, its change in total publication frequency was largely driven by 'other' types of publication, which increased from 0.51 publications per faculty member per year in 1979-1980 to 5.41 in 2019-2020, largely driven by Japanese language publication.ConclusionIn 2019-2020, pharmaceutical sciences faculty members largely published original papers in English, so postgraduate education should consider the future likelihood of graduates needing to publish in English.

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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