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IGSTK: A State Machine Architecture for an Open Source Software Toolkit for Image-Guided Surgery Applications
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The Image-Guided Surgery Toolkit (IGSTK) is an Open Source software project being developed under NIH/NIBIB funding. The toolkit will provide a common platform for implementing image-guided surgery applications and for fostering research in the field. The [...]

Open Source Software in the Development and Testing of an Image-Guided Robot System
No opinion
This paper describes the use of open source software in the development and testing of an image-guided robot system for small animal research, presented at MICCAI 2006. This system relied on a significant amount of open source software, including 3D [...]

Cerebral Cortical Thickness Estimation using the TINA
  Open-Source Image Analysis Environment
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This paper gives an overview of the use and development of the TINA open-source medical image analysis environment, with respect to the determination of human cerebral cortical thickness estimation from magnetic resonance images. The ultimate aim of TINA is [...]

IGSTK: Building High Quality Roads with Open Source Software
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This paper is a position statement on the benefits that an Open Source toolkit can bring to the field of image guided surgery. The particular example discussed here is the IGSTK toolkit. IGSTK is an open source software project designed for supporting the [...]

An Architecture Validation Toolset for Ensuring Patient Safety in an Open Source Software Toolkit for Image-Guided Surgery Applications
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As open source software projects gain acceptance in mission critical domains of a technology-enabled society, they must adapt their lightweight processes and tools to address the quality needs of these domains. One such domain is technology-supported [...]

FusionViewer: An Open Source Toolkit for Viewing Multimodality Images
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FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) [...]

Tetrahedral mesh generation for medical imaging
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We describe the open source implementation of an adaptive tetrahedral mesh generator particularly targeted for non-rigid FEM registration of MR images. While many medical imaging applications require robust mesh generation, there are few codes available. [...]

Guided Diffusion Tensor Tractography with GTRACT: A Validation Study
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A novel fiber tracking algorithm (GTRACT) was developed to enhance tracking through ambiguous regions where cross fibers, fiber merging or fanning may be occurring. The software was developed using several cross platform open-source toolkits (ITK, VTK, and [...]

MORPHIAS: Molecular Phenotyping Image Analysis System
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Visualizing metabolic phenotypes, tracking phenotype dynamics, and screening molecular interventions all require comprehensive, quantitative measures of micromolecular patterns across cell classes. In this project we develop an easy-to-use interface that [...]

BioImage Suite: An integrated medical image analysis suite
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BioImage Suite is an integrated image analysis software suite developed at Yale. It uses a combination of C++ and Tcl in the same fashion as that pioneered by the Visualization Toolkit (VTK) and it leverages both VTK and the Insight Toolkit. It has [...]

Real-Time Ultrasound Image Analysis for the Insight Toolkit
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We have successfully created a software environment in which ultrasound data can be manipulated by, ITK (the Insight Tool-Kit), in real-time. We were able to access each frame generated within the resident computer of a TerasonTM Ultrasound Machine, convert [...]

The NLM-Mayo Image Collection: Common Access to Uncommon Data
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For over two decades, the National Library of Medicine (NLM) has provided support for the collection of biomedical image data for use throughout the biomedical image, visualization and analysis community. Data collected during the Visible Human Project has [...]

Data, data everywhere, nor an image to read - Finding open image databases.
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Open Science includes access to both open source software/methodologies and open data. While there has been progress in open image databases, the results of these efforts are under-reported. As such, imaging scientists are unaware of the available data. In [...]

Improving The Oriented Image Class For Use In The Registration Framework
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The original design of the ITK registration framework was based around the itk::Image class, which assumed that the pixel axes were aligned with the coordinate system axes. The itk::OrientedImage was added later as a subclass, but problems remain with its [...]

Image Segmentation Project - Open source software practices class
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This document describes implementation of two Level-set segmentation algorithms using Insight Toolkit ITK . The algorithms chosen for implementation are are 1) Geodesic Active contour Levelset segmentation and 2) Shape Detection Levelset segmentation. The [...]

An image sampling framework for the ITK
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This document describes the implementation of image samplers using the Insight Toolkit ITK url{www.itk.org}. Image samplers take a set of `picks' from an image and store them in an array. A sample consists of the location of the pick (a point) and the [...]

An open-source real-time ultrasound reconstruction system for four-dimensional imaging of moving organs
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Four-dimensional imaging is a necessary step in computer-assisted interventions (CAI) performed on moving surgical targets, such as those located within the beating heart or influenced by respiratory motion. Ultrasound (US) is often the best imaging modality [...]

Cumulative Gaussian Curve Fitter for Boundary Parameterization
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We have previously developed an algorithm for locating boundaries in an image with sub-pixel resolution, as well as estimating boundary width and image intensity within the adjoining objects. The algorithm operates by finding the parameters of a cumulative [...]

An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open-source software
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This paper describes a new open-source tutorial for image-guided therapy (IGT) and medical robotics that is both accessible and hands-on using the LEGO Mindstorms NXT (a commercially available robotics kit) and 3D Slicer (an open-source application for [...]

Go-Go Gabor Gadgetry
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Although Gabor filtering is quite prevalent in the computer vision community for such tasks as texture segmentation and motion analysis, such capabilities are conspicuously absent from the Insight Toolkit. The contribution described in this paper attempts [...]

Entropy Image Filter
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This paper describes an intensity image filter for computing the entropy of pixel values contained within a neighborhood centered at each input pixel. The output image contains the calculated entropy for each input pixel location. This paper is accompanied [...]

Image Kernel Convolution
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Convolution is a basic operation in image analysis and the Insight Toolkit provides a well-framed mechanism for such operations (see Chapter 11 of the ITK Software Guide. The classes associated with this contribution are meant to simplify convolution [...]

Applying Image Mining to Support Gestational Age Determination
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The gestational age (GA) determination is one of the most used measures to guide diagnostics of specialists in neonatology to guarantee the newborn surveillance. However, the currently available methods have been subject to a number of evaluations and [...]

Alternative Memory Models for ITK Images
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By default ITK images use a contiguous memory model. This means pixel elements are stored in a single 1-D array, where each element is adjacent in memory to the previous element. However in some situations it is not desirable to use this memory model. This [...]

Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK
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The Allen Brain Atlas (ABA) project aims to create a cellular-resolution, genome-wide map of gene expression in the adult mouse brain. The resulting in situ hybridization (ISH) image data will be available free-of-charge to the public. Additionally, we [...]

The SIGN: A dynamic and extensible software framework for Image-Guided Therapy
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The software requirements for computer-aided navigation tools in image-guided therapy are becoming increasingly complex as a result of new possibilities in imaging and tracking hardware, novel application areas and regulatory restrictions. A new software [...]

Advanced Normalization Tools: V1.0
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We provide examples and highlights of Advanced Normalization Tools (ANTS) that address practical problems in real data. A variety of image and point similarity metrics and elastic, diffeomorphic, affine and other variations of transformation models are [...]

Variance Image Filter
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This paper describes an intensity image filter for computing the variance of pixel values contained within a neighborhood centered at each input pixel. The output image contains the calculated variance at each input pixel location. Variance calculations can [...]

Image Segmentation
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This document describes an algorithm implemented using the Insight Toolkit ITK www.itk.org. This paper is accompanied with the source code, input data, parameters and output data that the authors used for validating the algorithm described in this paper. [...]

A Fast Approximation to the Bilateral Filter for ITK
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This document describes an implementation of an alternative bilateral filtering algorithm in ITK. This class implements the fast bilateral filter algorithm in ITK by taking the input image and organizing it into the required data structure as an ITK Image [...]

An Image Filter for Counting Pixel Neighbors
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This papers describes an image filter that counts the number of neighbors a pixel has storing that value at the pixel's image index. Functionality is provided to 1) adjust the neighborhood size, 2) count only those pixels within a specific value range, and 3) [...]

Image Segmentation: Ventricle Isolation Using Region Growing
No opinion
This document describes the process used in implementing image segmentation through a region growing algorithm with the use of the Insight Toolkit (ITK) imaging program. The code used to implement the region growing algorithm is documented in the ITK Software [...]

Generalizing vesselness with respect to dimensionality and shape
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In this paper we present a generalization of Frangi's vesselness measure cite{Frangi1998} for the enhacement of M-dimensional shapes in N-dimensional images, together with the implementation of the corresponding Insight Toolkit (ITK) filter [...]

3D Voxel-Based Volumetric Image Registration with Volume-View Guidance
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In this article, we will present a novel interactive image registration technique using the 3D volumetric view as guidance throughout the registration process. The registration criterion used in this technique is the homogeneity of the color distribution on [...]

Direct Fourier Tomographic Reconstruction Image-To-Image Filter
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We present an open-source ITK implementation of a direct Fourier method for tomographic reconstruction, applicable to parallel-beam x-ray images. Direct Fourier reconstruction makes use of the central-slice theorem to build a polar 2D Fourier space from the [...]

CustusX: A Research Application for Image-Guided Therapy
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CustusX version 3 is an in-house application for research in image-guided therapy with a focus on intraoperative use and ultrasound imaging. It is built upon open source toolkits such as the Insight Toolkit (ITK), the Visualization Toolkit (VTK), Qt and [...]

Support for
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VoxBo (www.voxbo.org) is a distributed processing framework, developed at the Center of Functional Neuroimaging at the University of Penssylvania, with the purpose of processing and analyzing brain functional MRI data. VoxBo is written in C++, and it is [...]

Inverting deformation fields using a fixed point iteration scheme
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Being able to quickly compute the inverse of a deformation field is often useful in the context of medical image analysis. While ITK supports this functionality, the current algorithms are slow and do not always yield accurate results. In this paper we [...]

OpenIGTLink Protocol Version 2
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In this paper, we review the technical details of new features in OpenIGTLink version 2. OpenIGTLink is a free open-source network communication protocol designed for data exchange among devices and software. Since the first release of version 1.0 protocol [...]

The Generalised Image Fusion Toolkit (GIFT)
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Image fusion provides a mechanism to combine multiple images into a single representation to aid human visual perception and image processing tasks. Such algorithms endeavour to create a fused image containing the salient information from each source image, [...]

Computing Bone Morphometric Feature Maps from 3-Dimensional Images
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This document describes a new remote module implemented for the Insight Toolkit (ITK), itkBoneMorphometry. This module contains bone analysis filters that compute features from N-dimensional images that represent the internal architecture of bone. The [...]

Adapting the ITK Registration Framework to Fit Parametric Image Models
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The image registration framework in the Insight Tookit offers a powerful body of code for finding the optimal spatial transform that registers one image with another. However, ITK currently lacks a way to fit parametric models of image pixel values to an [...]

An ITK Implementation of the Symmetric Log-Domain Diffeomorphic Demons Algorithm
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This article provides an implementation of the symmetric log-domain diffeomorphic image registration algorithm, or symmetric demons algorithm for short. It generalizes Thirion's demons and the diffeomorphic demons algorithm. The main practical advantages of [...]

The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations
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This paper describes the Datatree module of BioImage Suite, that allows for rapid and flexible reslicing of images based on a user-defined tree structure that organizes image and transformation data as well as electrode localizations, image landmarks, and [...]

MUSiiC ToolKit 2.0: Bidirectional Real-time Software Framework for Advanced Interventional Ultrasound Research
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Ultrasound (US) imaging is a popular and convenient medical imaging modality thanks to its mobility, non-ionizing radiation, ease-of-use, and real-time acquisition. Conventional US imaging is frequently integrated with tracking systems and robotic systems in [...]

ITK Image IO interface with Apple iOS
No opinion
We have recently detailed the procedure for building ITK on the iOS. In this work, we contribute itkiOSImageIO , the necessary ITK class that provides the input/output (IO) interface with the repository of images stored on iOS Apple devices, such as the iPod [...]

MATITK: EXTENDING MATLAB WITH ITK
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To facilitate the analysis of medical image data in research environment, MATITK is developed to allow ITK algorithms to be called in MATLAB. ITK is a powerful open-source image analysis toolkit, but it requires the knowledge of C++ to use it. With the help [...]

Scale Invariant Feature Transform for n-Dimensional Images (n-SIFT)
No opinion
This document describes the implementation of several features previously developed[2], extending the 2D scale invariant feature transform (SIFT)[4, 5] for images of arbitrary dimensionality, such as 3D medical image volumes and time series, using ITK1. [...]

Itk::Transforms supporting spatial derivatives
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This document describes the use and implementation of first and second order spatial derivatives of coordinate transformations in the Insight Toolkit url{www.itk.org}). Spatial derivatives are useful for many types of regularising or penalty terms frequently [...]

Realistic And Efficient Brain-Skull Interaction Model For Brain Shift Computation
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In this paper we propose the usage of a very efficient contact implementation for modeling the brain-skull interaction. This contact algorithm is specially design for our Dynamic Relaxation solution method for solving soft-tissue registration problems. It [...]

Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation
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Modern medical imaging analyses often involve the concatenation of multiple steps, and neuroimaging analysis is no exception. The Java Image Science Toolkit (JIST) has provided a framework for both end users and engineers to synthesize processing modules into [...]

BioImage Suite: An integrated medical image analysis suite: An update
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BioImage Suite is an NIH-supported medical image analysis software suite developed at Yale. It leverages both the Visualization Toolkit (VTK) and the Insight Toolkit (ITK) and it includes many additional algorithms for image analysis especially in the areas [...]

The Lung Tissue Research Consortium:  An extensive open database containing histological, clinical, and radiological data to study chronic lung disease
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The Lung Tissue Research Consortium (LTRC) is an NHLBI sponsored project which is studying histological, radiological, and clinical data on patients with Chronic Obstructive Pulmonary Disease (COPD) and idiopathic pulmonary fibrosis (IPF). At completion, [...]

A programming environment for the development of modular 3D biomedical image processing applications
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ImageLib is a free object-oriented development environment destined to biomedical image processing. The software package contains a programming library (C++ language) and an MDI user interface (kernel). The major interest is to allow the creation of fully [...]

An ITK-based Implementation of the Stochastic Rank Correlation (SRC) Metric
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Recently, Birkfellner et al. proposed a novel image-to-image merit function (stochastic rank correlation, SRC) for robust intensity-based 2D/3D image registration. In this work, we summarize the basic idea of SRC, and present a generic ITK-based [...]

Unified framework for development, deployment and testing of image analysis algorithms
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Developing both graphical and command-line user interfaces for image analysis algorithms requires considerable effort. Generally developers provide limited to very rudimentary user interface controls to their users. These image analysis algorithms can only [...]

Simulink Libraries for Visual Programming of VTK and ITK
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We have created open-source Simulink block libraries for ITK and VTK that allow pipelines for these toolkits to be built in a visual, drag-and-drop style within MATLAB. Each block contains an instance of an ITK or VTK class. Any block connections and [...]

A Label Geometry Image Filter for Multiple Object Measurement
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The itkLabelGeometryImageFilter is a new ITK filter that enables the measurement of geometric features of labeled objects. It calculates features similar to the "regionprops" command of Matlab. It is related to the itkLabelStatisticsImageFilter in that both [...]

Flux driven medial curve extraction
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In this document it is described the implementation of the flux driven automatic centerline extraction algorithm proposed by Bouix et al. in 2004. This is based on a skeletonisation algorithm initially proposed by Siddiqi et al. in 2002, using properties of [...]

An open, clinically-validated database of 3D+t cine-MR images of the left ventricle with associated manual and automated segmentation
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In this paper, we describe a database of cine-MR (3D+t) images of the left ventricle. This database contains the voxel data, one automated and two manual segmentations for each sequence of images. The segmentations are validated from a clinical point of [...]


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ISSN 2327-770X
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