MeVisLab 3.0.x Community PDF-AddOn (2017-09-28 release)

These installers are self-contained, executable archives that automatically add all files of the MeVisLab Community PDF-Addon to an existing MeVisLab installation. This includes the source code as well as binary files. The target groups for these installers are MeVisLab newcomers and pure users that want to use the PDF-Addon features out-of-the-box. Future updates will be made available via Zenodo as well. This release contains installers for the follwing MeVisLab versions and operating systems: MeVisLab 3.0.x / Windows Visual Studio 2017 X64 MeVisLab 3.0.x / Windows Visual Studio 2015 X64 MeVisLab 3.0.x / Windows Visual Studio 2015 MeVisLab 3.0.x / Windows Visual Studio 2013 X64 MeVisLab 3.0.x / Linux 64Bit (tested with Ubuntu 14.04.2) MeVisLab 3.0.x / Mac OS X Intel 64Bit Important note: Error messages reagarding an incorrect MeVisLab version or a missing MeVisLab installation can be ignored if MeVisLab 3.0 or a sub-version (3.0.1 etc.) is installed. (The installers have been built with the latest MeVisLab version which might not be available for the public.) If the MeVisLab installation path could not be detected automatically, you must select it manually. In this case, select the path which contains the "Packages" folder as installation path. This is usually the standard installation path for applications + "MeVisLab" + Version Number (e.g., for Windows: C:\Program Files\MeVisLab3.0.1VC14-64). Installers for MeVisLab 2.8 are available from http://dx.doi.org/10.5281/zenodo.155381 Installers for MeVisLab 2.7 are available from http://dx.doi.org/10.5281/zenodo.47491 All those who are interested in being able to always use the latest version should connect their MeVisLab installation with the community sources which are hosted at GitHub [URL: https://github.com/MeVisLab/communitymodules/tree/master/Community; clone URL: https://github.com/MeVisLab/communitymodules.git]. This approach, however, requires compiling the source code and is intended only for experienced users or for users that are willing to become acquainted with MeVisLab. If you use this work for publications, please cite the following articles: Newe A. (2016) Enriching scientific publications with interactive 3D PDF: an integrated toolbox for creating ready-to-publish figures. PeerJ Computer Science 2:e64 https://doi.org/10.7717/peerj-cs.64 Newe A. (2015) Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files. PeerJ 3:e794 https://dx.doi.org/10.7717/peerj.794. PMID: 25780759

MeVisLab Community PDF-AddOn (2016-09-12 release)

These installers are self-contained, executable archives that automatically add all files of the MeVisLab Community PDF-Addon to an existing MeVisLab installation. This includes the source code as well as binary files. The target groups for these installers are MeVisLab newcomers and pure users that want to use the PDF-Addon features out-of-the-box. Future updates will be made available via Zenodo as well. This release contains installers for the follwing MeVisLab versions and operating systems: MeVisLab 2.8.x / Windows Visual Studio 2015 X64 MeVisLab 2.8.x / Windows Visual Studio 2013 X64 MeVisLab 2.8.x / Windows Visual Studio 2010 X64 MeVisLab 2.8.x / Linux 64Bit (tested with Ubuntu 14.04.2) MeVisLab 2.8.x / Mac OS X Intel 64Bit Important note: Error messages reagarding an incorrect MeVisLab version or a missing MeVisLab installation can be ignored if MeVisLab 2.8 or a sub-version (2.8.1 etc.) is installed. (The installers have been built with the latest MeVisLab version which might not be available for the public.) If the MeVisLab installation path could not be detected automatically, you must select it manually. In this case, select the path which contains the "Packages" folder as installation path. This is usually the standard installation path for applications + "MeVisLab" + Version Number (e.g., for Windows: C:\Program Files\MeVisLab2.8.2VC14-64). Installers for MeVisLab 3.0.x are available from http://dx.doi.org/10.5281/zenodo.998690 Installers for MeVisLab 2.7 are available from http://dx.doi.org/10.5281/zenodo.47491 All those who are interested in being able to always use the latest version should connect their MeVisLab installation with the community sources which are hosted at GitHub [URL: https://github.com/MeVisLab/communitymodules/tree/master/Community; clone URL: https://github.com/MeVisLab/communitymodules.git]. This approach, however, requires compiling the source code and is intended only for experienced users or for users that are willing to become acquainted with MeVisLab. If you use this work for publications, please cite the following articles: Newe A. (2016) Enriching scientific publications with interactive 3D PDF: an integrated toolbox for creating ready-to-publish figures. PeerJ Computer Science 2:e64 https://doi.org/10.7717/peerj-cs.64 Newe A. (2015) Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files. PeerJ 3:e794 https://dx.doi.org/10.7717/peerj.794. PMID: 25780759

Dramatyping: A generic algorithm for detecting reasonable temporal correlations between drug administration and lab value alterations

Abstract According to the World Health Organization, one of the criteria for the standardized assessment of case causality in adverse drug reactions is the temporal relationship between the intake of a drug and the occurrence of a reaction or a laboratory test abnormality. This article presents and describes an algorithm for the detection of a reasonable temporal correlation between the administration of a drug and the alteration of a laboratory value course. The algorithm is designed to process normalized lab values and is therefore universally applicable. It has a sensitivity of 0.932 for the detection of lab value courses that show changes in temporal correlation with the administration of a drug and it has a specificity of 0.967 for the detection of lab value courses that show no changes. Therefore the algorithm is appropriate to screen the data of electronic health records and to support human experts in revealing adverse drug reactions. A reference implementation in Python programming language is available

Dramatyping: a generic algorithm for detecting reasonable temporal correlations between drug administration and lab value alterations

According to the World Health Organization, one of the criteria for the standardized assessment of case causality in adverse drug reactions is the temporal relationship between the intake of a drug and the occurrence of a reaction or a laboratory test abnormality. This article presents and describes an algorithm for the detection of a reasonable temporal correlation between the administration of a drug and the alteration of a laboratory value course. The algorithm is designed to process normalized lab values and is therefore universally applicable. It has a sensitivity of 0.932 for the detection of lab value courses that show changes in temporal correlation with the administration of a drug and it has a specificity of 0.967 for the detection of lab value courses that show no changes. Therefore, the algorithm is appropriate to screen the data of electronic health records and to support human experts in revealing adverse drug reactions. A reference implementation in Python programming language is available

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

MeVisLab Community PDF-AddOn (2016-03-30 release) - DEPRECATED

<p><strong>ATTENTION!</strong></p> <p><strong>This version is deprecated. Please use the following resources for a newer version: </strong></p> <p><strong>http://dx.doi.org/10.5281/zenodo.</strong><strong>155381</strong> <strong>for MeVisLab 2.8(.x)</strong></p> <p><strong>http://dx.doi.org/10.5281/zenodo.47491 for MeVisLab 2.7(.x)</strong><br>  </p> <p> </p> <p>_____________________________________________________________________</p> <p> </p> <p>These installers are self-contained, executable archives that automatically add all files of the MeVisLab Community PDF-Addon to an existing MeVisLab installation. This includes the source code as well as binary files.</p> <p>The target groups for these installers are MeVisLab newcomers and pure users that want to use the PDF-Addon features out-of-the-box. Future updates will be made available via Zenodo as well.</p> <p>This release contains installers for the follwing MeVisLab versions and operating systems:</p> <ul> <li>MeVisLab 2.8 / Windows Visual Studio 2015 X64</li> <li>MeVisLab 2.8 / Windows Visual Studio 2013 X64</li> <li>MeVisLab 2.8 / Windows Visual Studio 2010 X64</li> <li>MeVisLab 2.8 / Linux 64Bit (tested with Ubuntu 14.04.2)</li> <li>MeVisLab 2.8 / Mac OS X Intel 64Bit</li> </ul> <p>All those who are interested in being able to always use the latest version should connect their MeVisLab installation with the community sources which are hosted at GitHub [URL: https://github.com/MeVisLab/communitymodules/tree/master/Community; clone URL: https://github.com/MeVisLab/communitymodules.git]. This approach, however, requires compiling the source code and is intended only for experienced users or for users that are willing to become acquainted with MeVisLab.</p> <p>If you use this work for publications, please cite the following article:</p> <p>Newe A. (2015) <em>Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files</em>. PeerJ 3:e794 https://dx.doi.org/10.7717/peerj.794. PMID: 25780759.</p> <p>Another article that describes this add-on in its entirety is currently under peer-review. A preprint can be downloaded here:</p> <p>Newe A. (2016) <em>Enriching scientific publications with interactive 3D PDF figures: A complete toolbox</em>. PeerJ PrePrints 4:e1594v2 https://doi.org/10.7287/peerj.preprints.1594v2</p

MeVisLab Community PDF-AddOn (2016-01-26 release) - DEPRECATED

<p><strong>ATTENTION!</strong></p> <p><strong>This version is deprecated. Please use the following resources for a newer version: </strong></p> <p><strong>http://dx.doi.org/10.5281/zenodo.</strong><strong>155381</strong> <strong>for MeVisLab 2.8(.x)</strong></p> <p><strong>http://dx.doi.org/10.5281/zenodo.47491 for MeVisLab 2.7(.x)</strong></p> <p> </p> <p>_____________________________________________________________________</p> <p> </p> <p>These installers are self-contained, executable archives that automatically add all files of the MeVisLab Community PDF-Addon to an existing MeVisLab installation. This includes the source code as well as binary files.</p> <p>The target groups for these installers are MeVisLab newcomers and pure users that want to use the PDF-Addon features out-of-the-box. Future updates will be made available via Zenodo as well.</p> <p>This release contains installers for the follwing MeVisLab versions and operating systems:</p> <ul> <li>MeVisLab 2.7(.x) / Windows Visual Studio 2013 X64</li> <li>MeVisLab 2.7(.x) / Linux 64Bit (tested with Ubuntu 14.04.2)</li> <li>MeVisLab 2.7(.x) / Mac OS X Intel 64Bit</li> </ul> <p><strong>Important note:</strong> Error messages reagarding an incorrect MeVisLab version or a missing MeVisLab installation can be ignored if MeVisLab 2.7 or a sub-version (2.7.1 etc.) is installed. The installers have been built with the latest MeVisLab version which might not be available to the public.</p> <p>All those who are interested in being able to always use the latest version should connect their MeVisLab installation with the community sources which are hosted at GitHub [URL: https://github.com/MeVisLab/communitymodules/tree/master/Community; clone URL: https://github.com/MeVisLab/communitymodules.git]. This approach, however, requires compiling the source code and is intended only for experienced users or for users that are willing to become acquainted with MeVisLab.</p> <p>If you use this work for publications, please cite the following article:</p> <p>Newe A. (2015) <em>Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files</em>. PeerJ 3:e794 https://dx.doi.org/10.7717/peerj.794. PMID: 25780759.</p

MeVisLab Community PDF-AddOn (2016-03-14 release)

<p>These installers are self-contained, executable archives that automatically add all files of the MeVisLab Community PDF-Addon to an existing MeVisLab installation. This includes the source code as well as binary files.</p> <p>The target groups for these installers are MeVisLab newcomers and pure users that want to use the PDF-Addon features out-of-the-box. Future updates will be made available via Zenodo as well.</p> <p>This release contains installers for the follwing MeVisLab versions and operating systems:</p> <ul> <li>MeVisLab 2.7(.x) / Windows Visual Studio 2013 X64</li> <li>MeVisLab 2.7(.x) / Linux 64Bit (tested with Ubuntu 14.04.2)</li> <li>MeVisLab 2.7(.x) / Mac OS X Intel 64Bit</li> </ul> <p><strong>Important note:</strong> Error messages reagarding an incorrect MeVisLab version or a missing MeVisLab installation can be ignored if MeVisLab 2.7 or a sub-version (2.7.1 etc.) is installed. The installers have been built with the latest MeVisLab version which might not be available to the public.</p> <p><strong>Installers for MeVisLab 2.8(.x) are available at http://dx.doi.org/10.5281/zenodo.155381</strong></p> <p>All those who are interested in being able to always use the latest version should connect their MeVisLab installation with the community sources which are hosted at GitHub [URL: https://github.com/MeVisLab/communitymodules/tree/master/Community; clone URL: https://github.com/MeVisLab/communitymodules.git]. This approach, however, requires compiling the source code and is intended only for experienced users or for users that are willing to become acquainted with MeVisLab.</p> <p>If you use this work for publications, please cite the following articles:</p> <p>Newe A. (2016) <em>Enriching scientific publications with interactive 3D PDF: an integrated toolbox for creating ready-to-publish figures</em>. PeerJ Computer Science 2:e64 https://doi.org/10.7717/peerj-cs.64</p> <p>Newe A. (2015) <em>Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files</em>. PeerJ 3:e794 https://dx.doi.org/10.7717/peerj.794. PMID: 25780759.</p

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

Background: The 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. Objective: The 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. Methods: A 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. Results: The 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. Conclusions: The 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

MeVisLab 3.0.x Community PDF-AddOn (2017-09-28 release)

<p>These installers are self-contained, executable archives that automatically add all files of the MeVisLab Community PDF-Addon to an existing MeVisLab installation. This includes the source code as well as binary files.</p> <p>The target groups for these installers are MeVisLab newcomers and pure users that want to use the PDF-Addon features out-of-the-box. Future updates will be made available via Zenodo as well.</p> <p>This release contains installers for the follwing MeVisLab versions and operating systems:</p> <ul> <li>MeVisLab 3.0.x / Windows Visual Studio 2017 X64</li> <li>MeVisLab 3.0.x / Windows Visual Studio 2015 X64</li> <li>MeVisLab 3.0.x / Windows Visual Studio 2015</li> <li>MeVisLab 3.0.x / Windows Visual Studio 2013 X64</li> <li>MeVisLab 3.0.x / Linux 64Bit (tested with Ubuntu 14.04.2)</li> <li>MeVisLab 3.0.x / Mac OS X Intel 64Bit</li> </ul> <p><em><strong>Important note:</strong> Error messages reagarding an incorrect MeVisLab version or a missing MeVisLab installation can be ignored if MeVisLab 3.0 or a sub-version (3.0.1 etc.) is installed. (The installers have been built with the latest MeVisLab version which might not be available for the public.) If the MeVisLab installation path could not be detected automatically, you must select it manually. In this case, select the path which contains the "Packages" folder as installation path. This is usually the standard installation path for applications + "MeVisLab" + Version Number (e.g., for Windows: C:\Program Files\MeVisLab3.0.1VC14-64)</em>.</p> <p><strong>Installers for MeVisLab 2.8 are available from http://dx.doi.org/10.5281/zenodo.155381</strong></p> <p><strong>Installers for MeVisLab 2.7 are available from http://dx.doi.org/10.5281/zenodo.47491</strong></p> <p>All those who are interested in being able to always use the latest version should connect their MeVisLab installation with the community sources which are hosted at GitHub [URL: https://github.com/MeVisLab/communitymodules/tree/master/Community; clone URL: https://github.com/MeVisLab/communitymodules.git]. This approach, however, requires compiling the source code and is intended only for experienced users or for users that are willing to become acquainted with MeVisLab.</p> <p>If you use this work for publications, please cite the following articles:</p> <p>Newe A. (2016) <em>Enriching scientific publications with interactive 3D PDF: an integrated toolbox for creating ready-to-publish figures</em>. PeerJ Computer Science 2:e64 https://doi.org/10.7717/peerj-cs.64</p> <p>Newe A. (2015) <em>Towards an easier creation of three-dimensional data for embedding into scholarly 3D PDF (Portable Document Format) files</em>. PeerJ 3:e794 https://dx.doi.org/10.7717/peerj.794. PMID: 25780759.</p