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

Ziv Yaniv; Bradley C Lowekamp; Hans J Johnson; Richard Beare

doi:10.1007/s10278-017-0037-8

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

Journal article

Open access

Peer reviewed

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

Ziv Yaniv, Bradley C Lowekamp, Hans J Johnson and Richard Beare

Journal of digital imaging, Vol.31(3), pp.290-303

06/2018

DOI: 10.1007/s10278-017-0037-8

PMCID: PMC5959828

PMID: 29181613

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https://doi.org/10.1007/s10278-017-0037-8View

Published (Version of record) Open Access

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 .

Cooperative Behavior

Diagnostic Imaging - methods

Humans

Image Processing, Computer-Assisted - instrumentation

Image Processing, Computer-Assisted - methods

Radiology - education

Reproducibility of Results

Research

Workflow

Details

Title: Subtitle: SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
Creators: Ziv Yaniv - National Institutes of Health
Bradley C Lowekamp - National Institutes of Health
Hans J Johnson - University of Iowa
Richard Beare - Monash University
Resource Type: Journal article
Publication Details: Journal of digital imaging, Vol.31(3), pp.290-303
DOI: 10.1007/s10278-017-0037-8
PMID: 29181613
PMCID: PMC5959828
NLM abbreviation: J Digit Imaging
ISSN: 0897-1889
eISSN: 1618-727X
Language: English
Date published: 06/2018
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Psychiatry
Record Identifier: 9984185467502771

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