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      The Design of SimpleITK

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          Abstract

          SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org.

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          Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

          We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.
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            Automated scientific software scripting with SWIG

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              Structural brain abnormalities in patients with schizophrenia and their healthy siblings.

              The authors sought to investigate the contribution of genotype on structural brain abnormalities in schizophrenia. Intracranial volumes and volumes of the cerebrum, white and gray matter, lateral and third ventricles, frontal lobes, caudate nucleus, amygdala, hippocampus, parahippocampal gyrus, and the cerebellum were measured in 32 same-sex siblings discordant for schizophrenia and 32 matched comparison subjects by means of magnetic resonance imaging. Third ventricle volumes did not differ between the schizophrenic patients and their healthy siblings. However, both had higher third ventricle volumes than did the comparison subjects. The schizophrenic patients had lower cerebrum volumes than did the comparison subjects, whereas the cerebrum volume of the healthy siblings did not significantly differ from the patients or comparison subjects. Additionally, patients with schizophrenia displayed a volume reduction of the frontal lobe gray matter and a volume increase of the caudate nuclei and lateral ventricles compared to both their healthy siblings and comparison subjects. Intracranial volume, CSF volume, or volumes of the cerebellum, amygdala, hippocampus, or the parahippocampal gyrus did not significantly differ among the patients, siblings, and comparison subjects. Healthy siblings share third ventricle enlargement with their affected relatives and may partially display a reduction in cerebral volume. These findings suggest that third ventricular enlargement, and to some extent cerebral volume decrease, may be related to genetic defects that produce a susceptibility to schizophrenia.
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                Author and article information

                Journal
                Front Neuroinform
                Front Neuroinform
                Front. Neuroinform.
                Frontiers in Neuroinformatics
                Frontiers Media S.A.
                1662-5196
                30 December 2013
                2013
                : 7
                : 45
                Affiliations
                [1] 1National Library of Medicine, Office of High Performance Computing and Communications, National Institutes of Health Bethesda, MD, USA
                [2] 2Medical Science and Computing Rockville, MD, USA
                [3] 3Kitware Inc. Clifton Park, NY, USA
                [4] 4Biomedical Engineering Department, Mayo Graduate School of Medicine Rochester, MN, USA
                Author notes

                Edited by: Hans J. Johnson, The University of Iowa, USA

                Reviewed by: Alexandre Gramfort, CNRS LTCI, France; Krzysztof Gorgolewski, Max Planck Institute for Human Cognitive and Brain Sciences, Germany

                *Correspondence: Bradley C. Lowekamp, National Library of Medicine, Office of High Performance Computing and Communications, BLDG 38A RM B1N30, 8600 Rockville Pike, Bethesda, 20894 MD, USA e-mail: blowekamp@ 123456mail.nih.gov

                This article was submitted to the journal Frontiers in Neuroinformatics.

                Article
                10.3389/fninf.2013.00045
                3874546
                24416015
                30fa60d5-3b64-4a48-9009-601284158535
                Copyright © 2013 Lowekamp, Chen, Ibáñez and Blezek.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 01 November 2013
                : 13 December 2013
                Page count
                Figures: 12, Tables: 0, Equations: 0, References: 23, Pages: 14, Words: 10121
                Categories
                Neuroscience
                Methods Article

                Neurosciences
                insight toolkit,software development,image processing software,image processing and analysis,software design,segmentation

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