Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Richard Beare, Bradley Lowekamp, Ziv Yaniv
Title: Image Segmentation, Registration and Characterization in R with SimpleITK
Abstract: Many types of medical and scientific experiments acquire raw data in the form of images. Various forms of image processing and image analysis are used to transform the raw image data into quantitative measures that are the basis of subsequent statistical analysis. In this article we describe the SimpleITK R package. SimpleITK is a simplified interface to the insight segmentation and registration toolkit (ITK). ITK is an open source C++ toolkit that has been actively developed over the past 18 years and is widely used by the medical image analysis community. SimpleITK provides packages for many interpreter environments, including R. Currently, it includes several hundred classes for image analysis including a wide range of image input and output, filtering operations, and higher level components for segmentation and registration. Using SimpleITK, development of complex combinations of image and statistical analysis procedures is feasible. This article includes several examples of computational image analysis tasks implemented using SimpleITK, including spherical marker localization, multi-modal image registration, segmentation evaluation, and cell image analysis.

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Paper: Image Segmentation, Registration and Characterization in R with SimpleITK     Download PDF (Downloads: 4481)
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DOI: 10.18637/jss.v086.i08

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.