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A filter to impose to the input image the minima defined in the marker image.
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.
This article illustrates the process of performing reproducible research with existing open source tools.
This document describes a contribution to the Insight Toolkit intended to perform landmark-based registration on two meshes. The method implemented here is restricted to meshes with a spherical geometry and topology. Please refer Wahba's paper for the [...]
An ITK Implementation of Physics-based Non-rigid Registration Method
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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
Published in The MIDAS Journal
Published in The MIDAS Journal
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 [...]
ITK Implementation Of The Minimum Error Image Thresholding Algorithm
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
Efficient N-Dimensional surface estimation using Crofton formula and run-length encoding
Published in The Insight Journal
Published in The Insight Journal
Unlike the measure of the area in 2D or of the volume in 3D, the perimeter and the surface are not easily measurable in a discretized image.
In this article we describe a method based on the Crofton formula to measure those two parameters in a discritized [...]
ItkImageFunctionImageFilter: A New Filter To Apply An itkImageFunction To Every Pixel In An itkImage
Published in The Insight Journal
Published in The Insight Journal
This document presents a new class to apply an itkImageFunction to every pixel in an itkImage. This functionality is almost identical to itkUnaryFunctorImageFilter, but it uses an itkImageFunction rather than an itk::Functor. As some functionalities in ITK [...]
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) [...]
An ITK-based Implementation of the Stochastic Rank Correlation (SRC) Metric
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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. [...]
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 [...]
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, [...]
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 [...]
Scalable Simple Linear Iterative Clustering (SSLIC) Using a Generic and Parallel Approach
Published in The Insight Journal
Published in The Insight Journal
Superpixel algorithms have proven to be a useful initial step for segmentation and subsequent processing of images, reducing computational complexity by replacing the use of expensive per-pixel primitives with a higher-level abstraction, superpixels. They [...]
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, [...]
Extracting Intersections of Coplanar Surfaces (Boolean-operation on touching meshes)
Published in The VTK Journal
Published in The VTK Journal
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 [...]
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, [...]
Thresholding is perhaps one of the most basic techniques in image processing. The Insight Toolkit (ITK) includes several threshold filters ranging from simple ones to Otsu based thresholding. Deep into the implementation of the Canny edge detection filter, [...]
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. [...]
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 [...]
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 [...]
Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter
Published in The Insight Journal
Published in The Insight Journal
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 [...]
N-Dimensional Computation of Strain Tensor Images in the Insight Toolkit
Published in The Insight Journal
Published in The Insight Journal
Strain quantifies local deformation of a solid body. In medical imaging, strain reflects how tissue deforms
under load. Or, it can quantify growth or atrophy of tissue, such as the growth of a tumor. Additionally,
strain from the transformation that results [...]
Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data
Published in The Insight Journal
Published in The Insight Journal
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, [...]
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 [...]
A patch-based framework for new ITK functionality: Joint fusion, denoising, and non-local super-resolution
Published in The Insight Journal
Published in The Insight Journal
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 [...]
Implementation of local structure tensor and enhancement anisotropic diffusion filters in ITK
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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 [...]
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, [...]
MR Parameter Map Suite: ITK Classes for Calculating Magnetic Resonance T2 and T1 Parameter Maps
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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 [...]
We have implemented filters for computing phase symmetry (PS) in ITK using steerable filters computed and applied in the Fourier domain. In some recent publications, phase symmetry has been shown to be a useful pre-processing measure for performing image [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
An Open Source, Fast Ultrasound B-Mode Implementation for Commodity Hardware
Published in The Insight Journal
Published in The Insight Journal
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
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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
Published in The MIDAS Journal
Published in The MIDAS Journal
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
Published in The MIDAS Journal
Published in The MIDAS Journal
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 [...]
