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      Dicomflex: A novel framework for efficient deployment of image analysis tools in radiological research

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          Abstract

          Objective

          Medical image processing tools in research are often developed from scratch without the use of predefined software structures, which potentially makes them less reliable and difficult to maintain. The objective here was to present and evaluate a novel framework (Dicomflex) for the deployment of tools with a uniform workflow, commonly encountered in medical image analysis.

          Materials and methods

          The object-oriented code was developed using Matlab. Dicomflex applications follow the common workflow of image-slice selection, user interaction, image processing, result visualization and progression to next slice. The framework consists of three important classes that host functionality, two configuration files and a front end that displays images, graphs and resulting data.

          Results

          So far, three different research tools have been created under the new framework. In comparison with previous Matlab analysis tools used at our institution, users of Dicomflex tools subjectively considered the learning phase to be shorter and handling to be simpler and more intuitive. They also highlighted the benefit and comfort of the standardized interface and predefined workflow. The framework-inherent handling of software versions was considered highly beneficial for maintenance as well as data and software management at different project stages. The clear separation of framework-related and unrelated code allows for a fast and more direct design of new tools in well-defined steps. The flexibility of the framework translates to a wide range of image processing tasks, such as segmentation, region-of-interest (ROI) analyses or computation of functional parameter maps, but is limited to 2D datasets.

          Conclusion

          Potential medical applications include the assessment of cardiac performance, detection of cerebrovascular disease or characterization of cancerous lesions. Dicomflex tools share a similar workflow and host the pertinent functions only. This may be relevant for many image processing needs in radiological research, where quick software deployment and reliability of results is essential.

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          Most cited references14

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          BioImage Suite: An integrated medical image analysis suite: An update.

          BioImage Suite is an NIH-supported medical image analysis software suite developed at Yale. It leverages both the Visualization Toolkit (VTK) and the Insight Toolkit (ITK) and it includes many additional algorithms for image analysis especially in the areas of segmentation, registration, diffusion weighted image processing and fMRI analysis. BioImage Suite has a user-friendly user interface developed in the Tcl scripting language. A final beta version is freely available for download.
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            Apparent diffusion coefficient threshold for delineation of ischemic core.

            MRI-based selection of patients for acute stroke interventions requires rapid accurate estimation of the infarct core on diffusion-weighted MRI. Typically used manual methods to delineate restricted diffusion lesions are subjective and time consuming. These limitations would be overcome by a fully automated method that can rapidly and objectively delineate the ischemic core. An automated method would require predefined criteria to identify the ischemic core. The aim of this study is to determine apparent diffusion coefficient-based criteria that can be implemented in a fully automated software solution for identification of the ischemic core. Imaging data from patients enrolled in the Diffusion and Perfusion Imaging Evaluation for Understanding Stroke Evolution (DEFUSE) study who had early revascularization following intravenous thrombolysis were included. The patients' baseline restricted diffusion and 30-day T2 -weighted fluid-attenuated inversion recovery lesions were manually delineated after coregistration. Parts of the restricted diffusion lesion that corresponded with 30-day infarct were considered ischemic core, whereas parts that corresponded with normal brain parenchyma at 30 days were considered noncore. The optimal apparent diffusion coefficient threshold to discriminate core from noncore voxels was determined by voxel-based receiver operating characteristics analysis using the Youden index. 51,045 diffusion positive voxels from 14 patients who met eligibility criteria were analyzed. The mean DWI lesion volume was 24 (± 23) ml. Of this, 18 (± 22) ml was ischemic core and 3 (± 5) ml was noncore. The remainder corresponded to preexisting gliosis, cerebrospinal fluid, or was lost to postinfarct atrophy. The apparent diffusion coefficient of core was lower than that of noncore voxels (P < 0.0001). The optimal threshold for identification of ischemic core was an apparent diffusion coefficient ≤ 620 × 10(-6) mm(2) /s (sensitivity 69% and specificity 78%). Our data suggest that the ischemic core can be identified with an absolute apparent diffusion coefficient threshold. This threshold can be implemented in image analysis software for fully automated segmentation of the ischemic core. © 2013 The Authors. International Journal of Stroke © 2013 World Stroke Organization.
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              ImgLib2—generic image processing in Java

              Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins. Availability: ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib. Supplementary Information: Supplementary data are available at Bioinformatics Online. Contact: saalfeld@mpi-cbg.de
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                Author and article information

                Contributors
                Role: ConceptualizationRole: MethodologyRole: SoftwareRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: ValidationRole: Writing – review & editing
                Role: ValidationRole: Writing – review & editing
                Role: Funding acquisitionRole: Project administrationRole: Supervision
                Role: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                11 September 2018
                2018
                : 13
                : 9
                : e0202974
                Affiliations
                [1 ] Department of Diagnostic and Interventional Radiology, University Hospital Leipzig, Leipzig, Saxony, Germany
                [2 ] Integrated Research and Treatment Center (IFB) Adiposity Diseases, Leipzig University Medical Center, Leipzig, Saxony, Germany
                NIH Clinical Center, UNITED STATES
                Author notes

                Competing Interests: HB has received a speaker honorarium from Siemens Healthcare. All other authors have no conflict of interest to declare.

                Article
                PONE-D-17-43325
                10.1371/journal.pone.0202974
                6133368
                30204771
                0d29c03e-113e-4069-88ec-9c0e343cc5a3
                © 2018 Stange et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 11 December 2017
                : 13 August 2018
                Page count
                Figures: 6, Tables: 1, Pages: 14
                Funding
                Funded by: Federal Ministry of Education and Research (BMBF), Germany
                Award ID: # 1EO1001
                Award Recipient :
                Funded by: Federal Ministry of Education and Research (BMBF), Germany
                Award ID: # 1EO1001
                Award Recipient :
                Grant support by the Federal Ministry of Education and Research (BMBF), Germany (# 1EO1001) is greatly acknowledged (RS, NL). We also acknowledge support from the German Research Foundation (DFG) and Leipzig University within the program of Open Access Publishing.
                Categories
                Research Article
                Computer and Information Sciences
                Computer Software
                Engineering and Technology
                Signal Processing
                Image Processing
                Medicine and Health Sciences
                Diagnostic Medicine
                Diagnostic Radiology
                Magnetic Resonance Imaging
                Research and Analysis Methods
                Imaging Techniques
                Diagnostic Radiology
                Magnetic Resonance Imaging
                Medicine and Health Sciences
                Radiology and Imaging
                Diagnostic Radiology
                Magnetic Resonance Imaging
                Biology and Life Sciences
                Biochemistry
                Lipids
                Fats
                Computer and Information Sciences
                Computer Architecture
                User Interfaces
                Research and Analysis Methods
                Imaging Techniques
                Computer and Information Sciences
                Software Engineering
                Software Tools
                Engineering and Technology
                Software Engineering
                Software Tools
                Computer and Information Sciences
                Data Visualization
                Infographics
                Graphs
                Custom metadata
                The complete Dicomflex framework is available online at https://github.com/Stangeroll/Dicomflex.

                Uncategorized
                Uncategorized

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