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.
Highlights
Images are an important source of quantitative information in many fields of research and many industrial, medical and scientific applications
In this article we introduce the SimpleITK package (The Insight Software Consortium 2018) for R(R Core Team 2018), which allows development of image analysis pipelines using R and a simplified interface to insight segmentation and registration toolkit (ITK)
SimpleITK allows us to query and set this dictionary as follows: Load a Digital Imaging and Communications in Medicine (DICOM) image and retrieve all the meta-data dictionary keys: R> img head(img$GetMetaDataKeys(), 5)
Summary
Images are an important source of quantitative information in many fields of research and many industrial, medical and scientific applications. Instruments in typical use include basic digital cameras in scenarios like security and wildlife monitoring, digital cameras associated with an ever increasing variety of microscopes, and medical imaging equipment such as magnetic resonance imaging (MRI), computed tomography (CT), ultrasound and X-ray. Other instruments, such as LIDAR, produce gridded data that may be useful to regard as an image in some scenarios. Designed for medical images, ITK has been successfully used in varied domains with data ranging from cell images to remote sensing images. ITK is a large, open source, C++ library which includes a wide variety of components for image analysis. ITK offers a high degree of customizability which, leads to a steep learning curve for developers and requires significant C++ experience
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