Image Segmentation, Registration and Characterization in R with SimpleITK
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 Sim...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Foundation for Open Access Statistics
2018-09-01
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| Series: | Journal of Statistical Software |
| Subjects: | |
| Online Access: | https://www.jstatsoft.org/index.php/jss/article/view/2734 |
| _version_ | 1818555101323722752 |
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| author | Richard Beare Bradley Lowekamp Ziv Yaniv |
| author_facet | Richard Beare Bradley Lowekamp Ziv Yaniv |
| author_sort | Richard Beare |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T09:48:47Z |
| format | Article |
| id | doaj.art-16b247d28d4742c28c33690c142819ff |
| institution | Directory Open Access Journal |
| issn | 1548-7660 |
| language | English |
| last_indexed | 2024-12-12T09:48:47Z |
| publishDate | 2018-09-01 |
| publisher | Foundation for Open Access Statistics |
| record_format | Article |
| series | Journal of Statistical Software |
| spelling | doaj.art-16b247d28d4742c28c33690c142819ff2022-12-22T00:28:19ZengFoundation for Open Access StatisticsJournal of Statistical Software1548-76602018-09-0186113510.18637/jss.v086.i081246Image Segmentation, Registration and Characterization in R with SimpleITKRichard BeareBradley LowekampZiv YanivMany 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.https://www.jstatsoft.org/index.php/jss/article/view/2734image processingimage segmentationimage registrationmedical imagingr |
| spellingShingle | Richard Beare Bradley Lowekamp Ziv Yaniv Image Segmentation, Registration and Characterization in R with SimpleITK Journal of Statistical Software image processing image segmentation image registration medical imaging r |
| title | Image Segmentation, Registration and Characterization in R with SimpleITK |
| title_full | Image Segmentation, Registration and Characterization in R with SimpleITK |
| title_fullStr | Image Segmentation, Registration and Characterization in R with SimpleITK |
| title_full_unstemmed | Image Segmentation, Registration and Characterization in R with SimpleITK |
| title_short | Image Segmentation, Registration and Characterization in R with SimpleITK |
| title_sort | image segmentation registration and characterization in r with simpleitk |
| topic | image processing image segmentation image registration medical imaging r |
| url | https://www.jstatsoft.org/index.php/jss/article/view/2734 |
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