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Journal of Imaging Informatics in Medicine

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Open Access 01-06-2018

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research

Authors: Ziv Yaniv, Bradley C. Lowekamp, Hans J. Johnson, Richard Beare

Published in: Journal of Imaging Informatics in Medicine | Issue 3/2018

Abstract

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks.

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Title: SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
Authors: Ziv Yaniv
Bradley C. Lowekamp
Hans J. Johnson
Richard Beare
Publication date: 01-06-2018
Publisher: Springer International Publishing
Published in: Journal of Imaging Informatics in Medicine / Issue 3/2018
Print ISSN: 2948-2925
Electronic ISSN: 2948-2933
DOI: https://doi.org/10.1007/s10278-017-0037-8

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SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research

Abstract

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