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MinimaImpositionImageFilter
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A filter to impose to the input image the minima defined in the marker image.

An ITK Implementation of Physics-based Non-rigid Registration Method
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As part of the ITK v4 project efforts, we have developed ITK filters for physics-based non-rigid registration (PBNRR), which satisfies the following requirements: account for tissue properties in the registration, improve accuracy compared to rigid [...]

Shape-based Interpolation of a Set of 2D Slices
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We implemented the shape-based interpolation method described by Raya and Udupa in 1990 for three-dimensional images, and created two standalone filters using the Insight Toolkit ITK. The image to be interpolated must be a 3D binary image which represents an [...]

Segmentation of the Left Ventricle from Cine MR Images Using a Comprehensive Approach
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Segmentation of the left ventricle is important in assessment of cardiac functional parameters. Currently, manual segmentation is the gold standard for acquiring these parameters and can be time-consuming. Therefore, accuracy and automation are two important [...]

Exponentiation Filters
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Two simple filters are contributed to compute the exponential of an image: the first one to raise the image to the power of a constant, the other one to raise the image to the power of the values provided in another image.

N4ITK:  Nick's N3 ITK Implementation For MRI Bias Field Correction
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Several algorithms exist for correcting the nonuniform intensity in magnetic resonance images caused by field inhomogeneities. These algorithms constitute important preprocessing steps for subsequent image analysis tasks. One such algorithm, known as [...]

Reproducible Research Training at Scipy 2014
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This article illustrates the process of performing reproducible research with existing open source tools.

ITK Implementation Of The Minimum Error Image Thresholding Algorithm
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An implementation of the minimum error thresholding algorithm is presented. In this implementation, two versions of the minimum error thresholding algorithm are made available, one utilizing a Gaussian- and the other utilizing a Poisson- mixture model. Two [...]

Introduction to ITK Resample In-Place Image Filter
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In this document we present an ITK image filter that outputs a new image with identical voxel contents but with modified physical space representation. The physical space representation of an image is modified to reflect the physical space transform on the [...]

Deconvolution: infrastructure and reference algorithms
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The deconvolution, also called deblurring, tries to revert the optical distortion introduced during the aquisition of the image. It is a family of image processing which can be classed in the larger family of image restoration. Deconvolution is a very [...]

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 [...]

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 [...]

Grayscale morphological attribute operations
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Morphological area attribute openings and closingscite{Cheng92,Vincent93a} are connected set operations that are able to remove parts of an image that meet certain criteria without changing the rest of the image. This article describes a number of classes [...]

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 [...]

Extracting Intersections of Coplanar Surfaces (Boolean-operation on touching meshes)
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The contribution to VTK presented in this article is specialized on the extraction of contact surfaces (CS). This extraction can be regarded as the intersection Boolean-operation of only touching meshes. The vtkCoplanarSurfaceExtractor filter produces either [...]

Automatic Junction Detection for Tubular Structures
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Junctions of tubular structures (vasculature, trachea, neuron, etc) in medical images are critical for the topology of these structures. Identification of them is helpful in many applications. For example, quantification of geometric vascular features, [...]

itkMultipleUnlabeledImagesToLabeledImageFilter
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This document describes a filter called itkMultipleUnlabeledImagesToLabeledImageFilter, which takes multiple images as input and generates a single image of labeled pixels. Pixels to be labeled for each image are determined by an intensity threshold. [...]

Kappa Sigma Clipping
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When an image is mostly composed of background pixels, most of the automatic thresholding methods are failing to produce a relevant threshold. This is mainly caused because one mode is over represented compared to the other in the histogram of the image. [...]

LookAt Transform Initializer and Oblique Section Image Filter
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This paper describes the ITK implementation of a transform initializer to produce a rigid 3-D transform able to center a given point on an arbitrary plane. The resultant transform allows the user to "look at" a point from a given direction. The resultant [...]

Anisotropic Diffusion in ITK
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Anisotropic Non-Linear Diffusion is a powerful image processing technique, which allows to simultaneously remove the noise and enhance sharp features in two or three dimensional images. Anisotropic Diffusion is understood here in the sense of Weickert, [...]

ND morphological contour interpolation
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This document describes a new class, itk::MorphologicalContourInterpolator, which implements a method proposed by Albu et al. in 2008. Interpolation is done by first determining correspondence between shapes on adjacent segmented slices by detecting overlaps, [...]

Anomalous Diffusion Paradigm for Image Denoising Process
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Anisotropic and isotropic diffusion equations have been extensively applied on biomedical image processing for many years and a great diversity of algorithm have been proposed by the scientific community. Here, it is available a recent new implementation of [...]

Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data
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This document describes a contribution to the Insight Toolkit intended to support the analysis of the principal components of data sets, optionally point data associated with the vertices of a mesh. This paper is accompanied with the source code, input data, [...]

Generating a Deformation Field from a Transform
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This document describes a new class that takes an doxygen{Transform} and evaluates the deformation at points in a user-defined region. The class is implemented using the Insight Toolkit url{www.itk.org}. This paper is accompanied with the source code, [...]

Implementation of local structure tensor and enhancement anisotropic diffusion filters in ITK
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This paper describes implementation of local structure tensor and anisotropic enhancement diffusion filters using the Insight Toolkit. The anisotropic diffusion filters are implemented using ITK's finite difference solver framework. The filters are used to [...]

Morphology with parabolic structuring elements
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Morphological erosion and dilation filters employ a structuring function, with flat structuring functions being the most common example. This article will use the term ``parabolic'', but much of the literature uses ``quadratic'' structuring functions are less [...]

MR Parameter Map Suite: ITK Classes for Calculating Magnetic Resonance T2 and T1 Parameter Maps
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This document describes a suite of new multi-threaded classes for calculating magnetic resonance (MR) T2 and T1 parameter maps implemented using the Insight Toolkit ITK (www.itk.org). Similar to MR diffusion tensor imaging (DTI), MR T2 and T1 parameter maps [...]

N-Dimensional Phase Unwrapping
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Although phase data can take on any value, it is generally only possible to measure phase as a principle value, i.e., wrapped within the range (-pi,pi]. Determining the unwrapped phase from its principle value is a topic of considerable interest in magnetic [...]

Exact Geometrical Predicate: Point in circle
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This document describes the implementation in ITK of the "point in circle" geometrical predicate. Based on Jonathan Shewchuk's work which implements an exact version of the predicate using standard floating point types and arithmetic, the implementation [...]

Laplacian Mesh Deformation
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Deforming a 3D surface mesh while preserving its local detail is useful for editing anatomical atlases or for mesh based segmentation. This contribution introduces new classes for performing hard and soft constraints deformation in a flexible design which [...]

Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter
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This document describes an ITK implementation of the adaptive patch-based image denoising algorithm described in cite{Manjon:2010aa}. This offering consists of the templated class itkPatchBasedDenoisingImageFilter interfaced through the DenoiseImage program [...]

A patch-based framework for new ITK functionality: Joint fusion, denoising, and non-local super-resolution
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In an earlier Insight Journal article, we introduced an ITK implementation of the adaptive patch-based image denoising algorithm described in [3]. We follow-up up that offering with a generalized non-local, patch-based ITK class framework and a refactored [...]

The Image-based Vascular Analysis Toolkit (IvanTk)
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This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an [...]

Laplace Beltrami Filter on QuadEdge Meshes
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A contribution to the Insight Toolkit intended to support the process of statistical analysis in Computational Anatomy. The methods included here operate on open or closed triagulated surfaces (represented by a QuadEdgeMesh). The filter assigns basis [...]

Efficient implementation of kernel filtering
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Kernel based filtering is one of the fundamental tools of image analysis and processing. A number of approaches have been developed over the years that allow efficient implementation of such filters even when the kernel size is large. This article reviews [...]

Tubular Geodesics using Oriented Flux: An ITK Implementation
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This document describes an ITK implementation of an interactive method for tracing curvilinear structures. The basic tools provided in this framework are an oriented flux-based tubularity measure and a geodesic path tracer that uses the fast marching [...]

ITK Image IO interface with Apple iOS
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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 [...]

Efficient contour detection in binary and label images
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ly in ITK, the only way to find the contour of the objects in a binary image is to use the BinaryErodeImageFilter, with a kernel of radius 1. This filter is a generic filter, made to support any shape and size of structuring element, and thus is not optimized [...]

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 [...]

A Spline-Driven Image Slicer
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In this article, a spline driven image slicer algorithm is presented. It is concretized through a vtkAlgorithm-inherited class that takes two inputs and gives two outputs. The first input is the volume from which the slice should reconstructed while the [...]

An Open Source, Fast Ultrasound B-Mode Implementation for Commodity Hardware
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This document describes an open source, high performance ultrasound B-Mode implementation based on the Insight Toolkit (ITK). ITK extensions are presented to calculate the radio-frequency (RF) signal envelope. A variety of 1D Fast Fourier Transform options [...]

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 [...]

Label object representation and manipulation with ITK
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Richard Beare has recently introduced a new filter to efficiently labelize the connected components with ITK, and has also proposed to use the run-length encoding used in that filter to implement some of the most useful binary mathematical morphology [...]

Implementation of a 3D thinning algorithm
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ITK currently comes with a 2D binary thinning (skeletonisation) method, but does not support 3D or higher. This paper documents a new itkBinaryThinningImageFilter3D and recommends to rename the current filter as itkBinaryThinningImageFilter2D. The 3D [...]

Minimally Interactive Knowledge-based Coronary Tracking in CTA using a Minimal Cost Path
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An algorithm for minimally interactive coronary artery tracking is presented. Tracking ability and accuracy results are demonstrated on 16 images CTA images. First, a region of interest is automatically selected and a denoising filter applied. Then, for each [...]

An entropy based multi-thresholding method for semi-automatic segmentation of liver tumors
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Liver cancer is the fifth most commonly diagnosed cancer and the third most common cause of death from cancer worldwide. A precise analysis of the lesions would help in the staging of the tumor and in the evaluation of the possible applicable therapies. In [...]


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