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Open AccessJournal ArticleDOI

The Design of SimpleITK

TLDR
SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages, bringing the capabilities of ITK to a wider audience.
Abstract
SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org.

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Journal ArticleDOI

NiftyNet: a deep-learning platform for medical imaging

TL;DR: An open-source platform is implemented based on TensorFlow APIs for deep learning in medical imaging domain that facilitates warm starts with established pre-trained networks, adapting existing neural network architectures to new problems, and rapid prototyping of new solutions.
Journal ArticleDOI

An automated approach for microplastics analysis using focal plane array (FPA) FTIR microscopy and image analysis

TL;DR: In this article, the analysis of imaging data derived from micro-Fourier transform infrared (μFTIR) microscopy is presented, which is a powerful tool allowing to analyze microplastics enriched on membrane filters.
Journal ArticleDOI

TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning

TL;DR: Support for 2D, 3D and 4D images such as X-ray, histopathology, CT, ultrasound and diffusion MRI and focus on reproducibility and traceability to encourage open-science practices.
Journal ArticleDOI

Reference database design for the automated analysis of microplastic samples based on Fourier transform infrared (FTIR) spectroscopy

TL;DR: An adaptable reference database, which can be applied to single-particle identification as well as methods like chemical imaging based on FTIR microscopy, and provides a reference point for data comparison with future and previous microplastic studies that are based on different databases.
Journal ArticleDOI

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

TL;DR: 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 is described.
References
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Book

Design Patterns: Elements of Reusable Object-Oriented Software

TL;DR: The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns, which most experienced OOP designers will find out they've known about patterns all along.
Book

The Logic of Scientific Discovery

Karl Popper
TL;DR: The Open Society and Its Enemies as discussed by the authors is regarded as one of Popper's most enduring books and contains insights and arguments that demand to be read to this day, as well as many of the ideas in the book.
Journal ArticleDOI

3D Slicer as an image computing platform for the Quantitative Imaging Network.

TL;DR: An overview of 3D Slicer is presented as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications and the utility of the platform in the scope of QIN is illustrated.
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