Dataset Information

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.

SUBMITTER: Beare R

PROVIDER: S-EPMC6168008 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Image Segmentation, Registration and Characterization in R with SimpleITK.

Beare Richard R Lowekamp Bradley B Yaniv Ziv Z

Journal of statistical software 20180801

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 d ...[more]

PMID: 30288153

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Project description:Over 200 georeferenced registered rephotographic compilations of the Faroe Islands are provided in this dataset. The position of each compilation is georeferenced and thus locatable on a map. Each compilation consists of a historical and a corresponding contemporary image showing the same scene. With steady object features, these two images of the same geolocation are aligned pixel accurately. In the summer of 2022, all contemporary images were photographed by A. Schaffland, while historical images were retrieved from the National Museum of Denmark collections. Images show Faroese landscape and cultural heritage sites, focusing on relevant areas when the historical images were taken, e.g., Kirkjubøur, Tórshavn, and Saksun. Historic images date from the end of the 19th century to the middle of the 20th century. The historical images were taken by scientists, surveyors, archaeologists, and painters. All historical images are in the public domain, have no known rights, or are shared under a CC license. The contemporary images by A. Schaffland are released under CC BY-NC-SA 4.0. The dataset is organized as a GIS project. Historic images, not already georeferenced, were referenced with street view services. All historical images were added to the GIS database, containing camera position, viewing direction, etc. Each compilation can be displayed as an arrow from the camera position along the view direction on a map. Contemporary images were registered to historical images using a specialized tool. None or only a suboptimal rephotograph could be taken for some historical images. These historical images are still added to the database together with all other original images, providing additional data for improvements in rephotography methods in the upcoming years. The resulting image pairs can be used in image registration, landscape change, urban development, and cultural heritage research. Further, the database can be used for public engagement in heritage and as a benchmark for further rephotography and time-series projects.

Dataset Information

Image Segmentation, Registration and Characterization in R with SimpleITK.

Publications

Image Segmentation, Registration and Characterization in R with SimpleITK.

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