Luis Ibanez

OpenIGTLink: an open network protocol for image-guided therapy environment

With increasing research on system integration for image‐guided therapy (IGT), there has been a strong demand for standardized communication among devices and software to share data such as target positions, images and device status.

The Image-Guided Surgery Toolkit IGSTK: An Open Source C++ Software Toolkit

This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers’ mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.

IGSTK: an open source software toolkit for image-guided surgery

Image-guided surgery applies leading-edge technology and clinical practices to provide better quality of life to patients who can benefit from minimally invasive procedures. Reliable software is a critical component of image-guided surgical applications, yet costly expertise and technology infrastructure barriers hamper current research and commercialization efforts in this area. IGSTK applies the open source development and delivery model to this problem. Agile and component-based software engineering principles reduce the costs and risks associated with adopting this new technology, resulting in a safe, inexpensive, robust, shareable, and reusable software infrastructure.

The Design of SimpleITK

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 ITKs complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITKs algorithms. It includes procedural methods, hides ITKs 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 ITKs 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.

Agile methods for open source safety-critical software

The introduction of software technology in a life‐dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety‐critical software development. Agile methods are flexible enough to encourage the right amount of ceremony; therefore if safety‐critical systems require greater emphasis on activities, such as formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code‐level quality than classic software engineering process models. We present our experiences on the image‐guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested almost a decade ago that they were not suitable for safety‐critical systems; we present our experiences as a case study for renewing the discussion. Copyright

Registration patterns: the generic framework for image registration of the insight toolkit

This paper describes the design and implementation of the generic framework for image registration contained in the National Library of Medicine NLM/NIH Segmentation and Registration Toolkit (ITK). The problem of image registration has been modeled here as a structure of pluggable components that can be easily interchanged. The rationale behind the framework is presented in this paper both from the image processing and software engineering points of view. ITK is an open source project that provides a platform for developing image processing and analysis applications. State of the art practices of software engineering have been used for the design, implementation and testing of the toolkit. The source code can be downloaded free of charge and used in academic and commercial applications.

ITK: enabling reproducible research and open science

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

Determination of discrete sampling grids with optimal topological and spectral properties

This paper proposes 2D, 3D and 4D discrete sampling grids with optimal topological and spectral properties. It is shown here that those grids have advantages with respect to the classically used ℤn grid. The proposed 3D grids are used to achieve surface extraction from volume data. Results are shown for a medical imaging application.

Integrating segmentation methods from the Insight Toolkit into a visualization application.

The Insight Toolkit (ITK) initiative from the National Library of Medicine has provided a suite of state-of-the-art segmentation and registration algorithms ideally suited to volume visualization and analysis. A volume visualization application that effectively utilizes these algorithms provides many benefits: it allows access to ITK functionality for non-programmers, it creates a vehicle for sharing and comparing segmentation techniques, and it serves as a visual debugger for algorithm developers. This paper describes the integration of image processing functionalities provided by the ITK into VolView, a visualization application for high performance volume rendering. A free version of this visualization application is publicly available and is available in the online version of this paper. The process for developing ITK plugins for VolView according to the publicly available API is described in detail, and an application of ITK VolView plugins to the segmentation of Abdominal Aortic Aneurysms (AAAs) is presented. The source code of the ITK plugins is also publicly available and it is included in the online version.

An open-source toolkit for the volumetric measurement of CT lung lesions

An open source lesion sizing toolkit has been developed with a general architecture for implementing lesion segmentation algorithms and a reference algorithm for segmenting solid and part-solid lesions from lung CT scans. The CT lung lesion segmentation algorithm detects four three-dimensional features corresponding to the lung wall, vasculature, lesion boundary edges, and low density background lung parenchyma. These features form boundaries and propagation zones that guide the evolution of a subsequent level set algorithm. User input is used to determine an initial seed point for the level set and users may also define a region of interest around the lesion. The methods are validated against 18 nodules using CT scans of an anthropomorphic thorax phantom simulating lung anatomy. The scans were acquired under differing scanner parameters to characterize algorithm behavior under varying acquisition protocols. We also validated repeatability using six clinical cases in which the patient was rescanned on the same day (zero volume change). The source code, data sets, and a running application are all provided under an unrestrictive license to encourage reproducibility and foster scientific exchange.