Format

Send to

Choose Destination
J Stat Softw. 2018 Aug;86. pii: 8. doi: 10.18637/jss.v086.i08. Epub 2018 Sep 4.

Image Segmentation, Registration and Characterization in R with SimpleITK.

Author information

1
Monash University, Department of Medicin, Monash Medical Centre, Clayton, Melbourne, Australia, 3168, Richard.Beare@monash.edu.
2
National Institutes of Health, Office of High Performance Computing and Communications, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894, United States of America, blowekamp@mail.nih.gov.
3
National Institutes of Health, Office of High Performance Computing and Communications, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894, United States of America, zivyaniv@nih.gov.

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.

KEYWORDS:

R; image processing; image registration; image segmentation; medical imaging

Supplemental Content

Full text links

Icon for PubMed Central
Loading ...
Support Center