Image Segmentation, Registration and Characterization in <i>R</i> with <b>SimpleITK</b>

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 <b>SimpleITK</b> R package. <b>SimpleITK</b> is a simplified interface to the insight segmentation and registration toolkit (<b>ITK</b>). <b>ITK</b> 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. <b>SimpleITK</b> 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 <b>SimpleITK</b>, development of complex combinations of image and statistical analysis procedures is feasible. This article includes several examples of computational image analysis tasks implemented using <b>SimpleITK</b>, including spherical marker localization, multi-modal image registration, segmentation evaluation, and cell image analysis.

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