Open-source Software Toolkit Research Articles

Analysing fundamental properties of marker-based vision system designs

This paper investigates fundamental properties of marker-based vision (MBV) systems. We present a theoretical analysis of the performance of basic tag designs which is extended through simulation to investigate the effects of different processing algorithms. Real-world data are processed and related to the simulated results. Image processing is performed using Cantag, an open-source software toolkit for building marker-based vision (MBV) systems that can identify and accurately locate printed markers in three dimensions. Cantag supports multiple fiducial shapes, payload types, data sizes and image processing algorithms in one framework. This paper explores the design space of tags within the Cantag system, and describes the design parameters and performance characteristics which an application writer can use to select the best tag system for any given scenario.

Robot Assisted Needle Placement: Application developed using an open source image guided surgery toolkit (IGSTK)

Using a robot system to position needles or needle shaped tools during clinical procedures such as biopsy, radio frequency ablation, and target drug delivery has a great potentials in increasing accuracy and speed of the process, and minimizing trauma to patient. This paper describes a robot assist needle placement system developed using Image Guided Surgery Toolkit (IGSTK). IGSTK is an open source software toolkit aimed at providing a robust and safe platform for researchers and clinicians for fast prototyping of image guided applications with minimum cost and effort

An open source software toolkit for image-guided surgery

An open source software toolkit for image-guided surgery

Image-based guidance for minimally invasive surgical atrial fibrillation ablation

Atrial fibrillation (AF) is the most common arrhythmia and results in an increased risk of ischaemic stroke. Recently, a European consortium has developed a new ablation device for minimally invasive surgical AF treatment. The device is controlled by a medical robot. Due to the minimal invasive usage, surgery using the new device needs appropriate navigation support. In this paper, we describe an image-based navigation application to guide the new device intraoperatively. The navigation procedure is based on intraoperative ultrasound. Variations in the position of the ablation device are transferred from the software controlling the robot to the navigation system. Due to the flexibility of the ablation device, a deformation model predicts the behaviour during repositioning. Ablation lines are interactively planned. Actually burned ablation lines are visualized during surgery. Several in vitro and ex vivo experimental set-ups were built up to test the feasibility. The navigation workflow was implemented into navigation software using well-known open-source software toolkits. The navigation system has been integrated and tested successfully within the overall system. The ablation device could be localized on in vitro and ex vivo ultrasound images. The performed trials proved the applicability of the navigation procedure. More in vivo tests are currently being performed to make the new device and the described navigation procedure ready for clinical use.

A Statistical Toolkit for Data Analysis

The present project aims to develop an open-source and object-oriented software Toolkit for statistical data analysis. Its statistical testing component contains a variety of Goodness-of-Fit tests, from Chi-squared to Kolmogorov-Smirnov, to less known, but generally much more powerful tests such as Anderson-Darling, Goodman, Fisz-Cramer-von Mises, Kuiper, Tiku. Thanks to the component-based design and the usage of the standard abstract interfaces for data analysis, this tool can be used by other data analysis systems or integrated in experimental software frameworks. This Toolkit has been released and is downloadable from the web. In this paper we describe the statistical details of the algorithms, the computational features of the Toolkit and describe the code validation.

Clustering Based Cardiac Resynchronization Therapy Prediction using Open Source Toolkit PRTools

We propose a novel framework at MICCAI 2005 to predict pacing sites in the left ventricle (LV) of a heart. This framework can be used to assist pacemaker implantation and programming in cardiac resynchronization therapy (CRT) that is a widely adopted therapy for heart failure patients. Hierarchical agglomerative clustering technique is performed to the time series of LV wall thickness to identify pacing site candidates. Meanwhile, pearson correlation coefficients of wall motion series show the dissimilarity between them. These main components of our clustering based prediction framework are implemented by using open source software toolkit PRTools.

IGSTK: Development Process and Project Management Best Practices for an Open Source Software Toolkit for Image-Guided Surgery Applications

Open source technologies are increasing in popularity for software development. Many open source projects rely on skilled development teams whose members are distributed throughout the world. Often, agile development methods are employed by these teams, as the focus is on concurrent development and fast production over requirements management and quality assurance. The image-guided surgery toolkit (IGSTK) is an open source development project that relies on the collaboration of a skilled and distributed development team, yet addresses a domain that demands managing requirements as well as implementing a high degree of robustness and addressing safety concerns. Due to this unique cross-section of open source technology and the surgical domain, the IGSTK team has developed a set of best practices and requirements techniques to augment commonly applied agile methods. This paper presents the lessons we have learned as we have engaged in the software development process.

Integrating modelling architecture: a declarative framework for multi-paradigm, multi-scale ecological modelling

Multiple modelling paradigms are necessary to formulate crucial modelling problems in modern environmental science. Modelling paradigms help researchers to conceive, formulate and solve problems by providing semantic structures to organise their view of a system or process. An unusually large array of different paradigms is used in Ecology, reflecting the complexity and variety of the natural world. As a result of this, multi-disciplinary problems in particular suffer of representational difficulties that prevent them to be approached efficiently with available software toolkits. In this paper I outline the theoretical aspects of model compatibility in the operational aspects of representation, scale and domain, and I describe the Integrating Modelling Architecture (IMA), a declarative framework and an open-source software toolkit to allow integrated meta-modelling. The IMA allows to specify generic model components using a common markup language, and loads paradigm-specific grammars that can be extended to support multiple paradigms. Among the project's goals are: (1) allow web-based integration of models and state-of-the-art resources distributed across a wide area network; (2) integrate and reuse existing simulation programs and toolkits; (3) allow integration between independently developed models adopting different modelling paradigms, scales, and domains; and (4) provide extendible, efficient and clear abstractions to conceptualise and solve complex, multiple-paradigm modelling problems in environmental science. At the end of the paper I argue that an integrative meta-modelling paradigm allows us to formulate and solve new important problems, and illustrate some of the new modelling scenarios enabled by the availability of these new concepts and tools.