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Probability Distributions for the Insight Toolkit
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Probability distributions are a key component of clinical research. One only has to make a cursory review of clinical literature to realize that nearly all clinical publications reference some sort of statistical test; be it t-test, chi-squared test, or [...]

RPI OSSP Ventricle ConnectedThreshold Segmentation
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Image Segmentation: Ventricle Isolation Using Region Growing
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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 [...]

Permute Axes Transform for ITK
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The current ITK release (2.8) already contains a filter that enables permuting coordinate axes of an image: PermuteAxesImageFilter. PermuteAxesTransform provides similar functionality in form if ITK transform. It enables permuting axes as a part of image [...]

Phase Correlation Method for ITK
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Phase Correlation Method (PCM or SPOMF - Symmetric Phase-Only Matched Filter) is a well known image registration method, that exploits Fourier Shift Theorem property of Fourier Transform. Even though it is limited to estimate only shifts between two images, [...]

Finite Element Modeling of the Pulse Wave propagation in the aorta for simulation of the Pulse Wave Imaging (PWI) method
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A large number of pathological conditions result in significant changes of the mechanical properties of the aortic wall. Using the Pulse Wave Velocity (PWV) as an indicator of aortic stiffness has been proposed for several decades. Pulse Wave Imaging (PWI) is [...]

ITK-Based Implementation of Two-Projection 2D/3D Registration Method with an Application in Patient Setup for External Beam Radiotherapy
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This document describes an ITK-based implementation of intensity-based 2D/3D rigid image registration for patient setup assessment in external beam radiotherapy. The registration framework was designed to simultaneously register two projection images to a 3D [...]

Explicit Deformable Model in VTK
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This document describes a set of classes that designs a generic explicit deformable model in VTK. The iterative mechanism is first introduced through an inheritance of the vtkPolyDataAlgorithm class. This vtkIterativePolyDataAlgorithm is then a base for an [...]

Importing Contours from DICOM-RT Structure Sets with ITK4
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This paper presents code for reading contours from DICOM RT structure set files into binary labels. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image analysis [...]

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 [...]

Polar Transforms for ITK
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Polar transform is a geometric transform, that transforms points form cartesian coordinates to so-called polar coordinates. In case of 2D space, a point in polar coordinate system is addressed by radius and angle. In image processing, polar transform is [...]

Anisotropic Fast Marching in ITK
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The Fast Marching algorithm is an efficient numerical method for computing the distance and shortest path between points of a domain. For that purpose, it solves a front propagation problem, which can be of interest in itself. The method has numerous [...]

Giving streaming and multi-threading capabilities to non-streamable ITK filters
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This document describes a filter able to give streaming and multi-threading capabilities to those filters that can not be easily streamed or multi-threaded. The goal of this document is to explain the implementation of this filter, and how it can be used to [...]

A MultipleImageIterator for iterating over multiple images simultaneously
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Several applications such as multi-atlas segmentation require frequent iteration over multiple image volumes at the same time. Doing so with the regular ITK iterators is tedious and error prone as it requires updating each iterator at end of each iteration. [...]

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 [...]

Digital Topology
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This documents describes a set of classes to integrate digital topology in the Insight Toolkit, with an application to homotopic thinning. The skeletonization filter implemented using our set of classes is twice as fast as BinaryThinningImageFilter and can [...]

An Intelligent cluster-based segmentation using Wavelet Features:Application to Medical Images
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Segmentation forms the onset for image analysis especially for medical images, making any abnormalities in tissues distinctly visible. Possible application includes the detection of tumor boundary in SPECT, MRI or electron MRI (EMRI). Nevertheless, tumors [...]

Big Data Analysis and Visualization with Open Source Tools
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This talk presents the Open-Source toolkits developed by Kitware for big data analysis.

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 [...]

Unsupervised Segmentation for Myofiber Counting in Immunofluorescent Microscopy Images
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The gold standard for measuring muscle regeneration in muscular dystrophy therapies is counting the number of dystrophin-positive muscle fibers on a cryostat muscle section immunostained for dystrophin. The standard process of manually counting a few thousand [...]

N-D $C^k$ B-Spline Scattered Data Approximation
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Since the 1970's B-splines have evolved to become the {em de facto} standard for curve and surface representation due to many of their salient properties. Conventional least-squares scattered data fitting techniques for B-splines require the inversion [...]

Evaluation of the Dynamic Deformable Elastic Template model for the segmentation of the heart in MRI sequences
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We introduce a bio-inspired dynamic deformable (DET) model based on the equation of dynamics and including temporal smoothness constraints. The behaviour and characteristics of the dynamic DET model is studied in the context of the semi automatic [...]

Multi-Atlas Brain MRI Segmentation with Multiway Cut
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Characterization of anatomical structure of the brain and effi cient algorithms for automatically analyzing brain MRI have gained an increasing interest in recent years. In this paper, we propose an algorithm that automatically segments the anatomical [...]

N-D Linear Time Exact Signed Euclidean Distance Transform
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Fast computation of distance transforms find direct application in various computer vision problems. Currently there exists two image filters in the ITK library which can be used to generate distance maps. Unfortunately, these filters produce only [...]

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, [...]

Stochastic Fractal Dimension Image
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Fractal analysis for medical image classification and analysis was introduced in cite{Chen1989}. According to the authors, when viewed as an intensity surface, Mandelbrot's fractal theory provides an informative framework for characterizing such a surface. [...]

Creation and Demonstration of a Framework for Handling Paths in ITK
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A hierarchy of path data types and basic path filters were added to ITK, providing a general framework for curves that map a scalar value to a point in n-dimensional space. The framework supports curves that are either continuous (parametric curves) or [...]

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 [...]

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 [...]

Integration of Geometrical Boundary Conditions on Soft Tissue Characterization under large deformation
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Soft tissue characterization with finite element (FE) modeling is important to develop a realistic model for medical simulation, since it is possible to display complex tool-tissue interactions during medical interventions. However, it is difficult to [...]

Scene Graph: Visualization of Coordinate Systems in the Image Guided Surgical Toolkit
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In a surgical environment, there are many tools and objects (including the patient) being used. In a computer-aided surgery, the position of each of these tools in the operating room is very critical and generally will be tracked in their own coordinate [...]

Validation of Liver Tumor Segmentation in CT Scans by Relating Manual and Algorithmic Performance - A Preliminary Study
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The development of segmentation algorithms for liver tumors in CT scans has found growing attention in recent years. The validation of these methods, however, is often treated as a subordinate task. In this article, we review existing approaches and present [...]

Run-Length Matrices For Texture Analysis
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Texture analysis provides quantitative information describing properties in images such as coarseness and smoothness. Two common quantification schemes are based on co-occurence matrices and run-length matrices. Although the co-occurence measures are [...]

Extension to OpenIGTLink; Smart Socket Connection, XML as Message, Logging, and One-to-multi Relaying
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We extended OpenIGTLink with following useful features; 1) AgentSocket class to capsulate socket initiation for smarter socket connection with try-catch implementation, 2) XmlMessage class to handle an XML text message. Using this extension, we will implement [...]

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 [...]

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 [...]

Reader/Writer for Analyze Object Maps for ITK
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This document describes an addition to the Image IO Library of the Insight Toolkit (ITK). ITK has been able to read in Analyze image files but not the Analyze Object Maps that correspond to the images. Analyze Object maps define regions of interest that are [...]

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 [...]

N-Dimensional Path Optimization:  The Implementation of a Novel Algorithm in ITK
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Using the path framework we previously added to ITK, we implemented a novel algorithm for n-dimensional path optimization, which we call the ND Swath (NDS). NDS uses dynamic programming to globally optimize the placement of a path within an image, subject to [...]

Introducing Dice, Jaccard, and Other Label Overlap Measures To ITK
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Although the KappaStatisticImageToImageMetric can be used to obtain the Dice metric (or mean overlap), there are other related measurements that are useful for evaluating results derived from various image analysis tasks. These measures include the target [...]

Knowledge-Based Segmentation of Brain MRI Scans Using the Insight Toolkit
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An Insight Toolkit (ITK) implementation of our knowledgebased segmentation algorithm applied to brain MRI scans is presented in this paper. Our algorithm is a refinement of the work of Teo, Saprio, and Wandall. The basic idea is to incorporate prior [...]

Impact of motion correction on the quantitative analysis of DCE-MR Images
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Dynamic magnetic resonance imaging (DCE-MRI) carried out with contrast media such as Gd-chelate complex (Gd-DTPA) allows the non-invasive assessment of microcirculatory characteristics of malignant lesions. Quantitative estimation of lesion [...]

MITK and 3DMed : An Integrated Platform Applicable for the Development of Computer Assisted Intervention Systems
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This paper introduces an integrated 3D medical image processing and analyzing software platform which is open interface and freely available. The platform consists of the Medical Imaging Toolkit (MITK) and the 3-Dimensional Medical Image Processing [...]

Segmentation of Head and Neck CT Scans Using Atlas-based Level Set Method
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In this paper, we present an atlas-based level set automatic method for segmenting anatomical structures in head and neck CT data, such as mandible and brainstem. The proposed method is a hybrid method that combines two aspects. First, we register the atlas [...]

Endocardial Segmentation using Structured Random Forests in 3D Echocardiography
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Segmentation of the left ventricle endocardium in 3D echocardiography is a critical step for the diagnosis of heart disease. Although recent work has shown effective endocardial edge detection, these techniques still preserve spurious anatomical edge [...]

Automatic Brain Tissue Segmentation of Multi-sequence MR Images Using Random Decision Forests
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This work is integrated in the MICCAI Grand Challenge: MR Brain Image Segmentation 2013. It aims for the automatic segmentation of brain into Cerebrospinal fluid (CSF), Gray matter (GM) and White matter (WM). The provided dataset contains patients with white [...]

The graph windowed Fourier transform: a tool to quantify the gyrification of the cerebral cortex
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The Gyrification Index (GI) quantifies the amount of folding of a cortical surface. In this paper, we show the efficiency of spectral analysis to perform such a task, and in particular we explain how the graph windowed Fourier transform can be used as a tool [...]

ITK Tutorial Presentation Slides
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This course introduces attendees to select open-source efforts in the field of medical image analysis. Opportunities for users and developers are presented. The course particularly focuses on the open-source Insight Toolkit (ITK) for medical image [...]

Conformal Flattening ITK Filter
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This paper describes the Insight Toolkit (ITK) Conformal Flattening filter: itkConformalFlatteningFilter. This ITK filter is an implementation of a paper by Sigurd Angenent, et al., “On the Laplace-Beltrami Operator and Brain Surface Flattening”. This [...]

An ITK Filter for Bayesian Segmentation:  itkBayesianClassifierImageFilter
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An Insight Toolkit (ITK) filter for image segmentation with applications to brain MRI scans is presented in this paper. Previously, we showed how ITK could be used to implement our algorithm. This paper presents our new ITK filter for Bayesian segmentation [...]

A DICOM-based Software Infrastructure for Data Archiving
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In this paper , we propose an extension to the National Library of Medicine's Insight Segmentation and Registration Toolkit (ITK. www.itk.org) with a companion image access and archival system that merges the image transfer capabilities of DICOM with DSpace [...]

Live-Wire-ing the Insight Toolkit with Intelligent Scissors
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Semi-automatic image segmentation algorithms depend on interaction with the user to accurately define a region of interest within an image. Once such method is a dynamic programming approach called {em Intelligent Scissors} developed by Mortenson and Barret [...]

Well-Composedness and the Topological Repairing of 2-D and 3-D Digital Images
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In an earlier submission, we considered 2-D and 3-D digital binary images topologically characterized by their well-composedness. Well-composed images exhibit important topological and geometrical properties not shared by their ill-composed counterparts. [...]

Gridding Graphic Graticules
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Certain classes of images find disparate use amongst members of the ITK community for such purposes as visualization, simulation, testing, etc. Currently there exists two derived classes from the ImageSource class used for generating specific images for [...]

A Mix-resolution Bone-related Statistical Deformable Model (mBr-SDM) for Soft Tissue Prediction in Orthognathic Surgery Planning
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In this paper, we propose a Mix-resolution Bone-related Statistical Deformable Model (mBr-SDM) to improve the predicting accuracy of orthognathic surgery, particularly for the main deformation region. Mix-resolution Br-SDM consists of two separate Br-SDM of [...]

MS Lesion Segmentation based on Hidden Markov Chains
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In this paper, we present a new automatic robust algorithm to segment multimodal brain MR images with Multiple Sclerosis (MS) lesions. The method performs tissue classification using a Hidden Markov Chain (HMC) model and detects MS lesions as outliers to the [...]

Interactive Liver Tumor Segmentation Using Graph-cuts and Watershed
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We present in this paper an application of minimal surfaces and Markov random fields to the segmentation of liver tumors. The originality of the work consists in applying these models to the region adjacency graph of a watershed transform. We detail [...]

Information-Theoretic Directly Manipulated Free-Form Deformation Labeled Point-Set Registration
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Our previous contributions to the ITK community include a generalized B-spline approximation scheme as well as a generalized information-theoretic measure for assessing point-set correspondence known as the Jensen-Havrda-Charvat-Tsallis (JHCT) divergence. In [...]

Carotid Lumen Segmentation Based on Tubular Anisotropy and Contours Without Edges
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We present a semi-automatic algorithm for Carotid lumen segmentation on CTA images. Our method is based on a variant of the minimal path method that models the vessel as a centerline and boundary. This is done by adding one dimension for the local radius [...]

Integration of a Robotic Endoscope Holder with the Surgical Assistant Workstation Software Framework
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We have integrated the Philips Research robot arm with the Johns Hopkins cisst library, an open-source platform for computer assisted surgical intervention, for assistance during minimally invasive cardiac surgery using image-based steering of an endoscope. [...]

Creating a 2D Active Shape Model Using itk::ImagePCAShapeModelEstimator
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Although many variations of active contour segmentation algorithms exist, most are based on solely edge criteria and breakdown or leak at weak boundaries. One solution to this problem is constraining the segmented area to only statistically possible shapes [...]

Voxelizer plug-in for Blender
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This document describes a plug-in for Blender (www.blender.org) that allows to rasterize 3D mesh objects into 3D voxel data, i. e. it allows to voxelize Blender meshes. In 2D, this process can be compared to rasterization of vector graphics into pixel [...]

A VTK Algorithm for the Computation of the Hausdorff Distance
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The Hausdorff distance is a measure of the distance between sets of points. There are many advantages to using this metric compared to other similarity measures. This document describes a VTK class for computing the Hausdorff Distance between two sets of [...]

Dose Painting with a Variable Collimator for the Small Animal Radiation Research Platform (SARRP)
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The goal of radiation treatment is to irradiate cancer cells (i.e., a target region) without destroying adjacent healthy tissue. Thus, it is advantageous to form the beam so that it best approximates the target, thereby reducing the amount of dose absorbed in [...]

Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
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Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]

Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
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Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]

OpenTissue - An Open Source Toolkit for Physics-Based Animation
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OpenTissue is a multidisciplinary, open source programming toolkit for physics-based simulation, collision detection, scientific visualization, and medical imaging. The toolkit was initiated in 2001, is driven by academia, and is used by several [...]

A Novel Information-Theoretic Point-Set Measure Based on the Jensen-Havrda-Charvat-Tsallis Divergence
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A novel point-set registration algorithm was proposed in [6] based on minimization of the Jensen-Shannon divergence. In this contribution, we generalize this Jensen-Shannon divergence point-set measure framework to the Jensen-Havrda-Charvat-Tsallis [...]

Gaussian Interpolation
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In this submission, we offer the GaussianInterpolationImageFunction which adds to the growing collection of existing interpolation algorithms in ITK for resampling scalar images such as the LinearInterpolateImageFunction, BSplineInterpolateImageFunction, and [...]

Well-Composed Image Filters for Repairing 2-D and 3-D Binary Images
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We consider 2-D and 3-D digital binary images characterized by their well-composedness. Well-composed images exhibit important topological and geometrical properties not shared by their ill-composed counterparts. These properties have important [...]

A generic interpolator for multi-label images
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We present a generic interpolator for label images. The basic idea is to interpolate each label with an ordinary image interpolator, and return the label with the highest value. This is the idea used by the itk::LabelImageGaussianInterpolateImageFunction [...]

Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
No opinion
Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]

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 [...]

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 [...]

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 [...]

Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge
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Within the framework of the CETUS challenge, forty-five 3D echocardiographic datasets have been acquired and segmented independently by three clinical experts from different hospitals. The goal was to generate a well-established ground truth of validated [...]

Computational Geometry Computation and KNN Segmentation in ITK
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This work describes the implementation of computational geometry algorithms developed within the Insight Toolkit (ITK): Distance Transform (DT), Voronoi diagrams, k Nearest Neighbor (kNN) transform, and finally a K Nearest Neighbor classifier for multichannel [...]

Integration of Fuzzy Mathematical Morphology and Fuzzy Spatial Relationships into ITK
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The aim of this paper is to present the integration of new filters computing fuzzy mathematical morphology and spatial relationships into ITK and to share our experience with the Open source community. Our implementation architecture follows the essential [...]

BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit
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The University of Iowa’s Psychiatric Iowa Neuroimaging Consortium (PINC) has developed a program for mutual information registration of 3D brain imaging data using ITK classes, called BRAINSFit. We have written a helper class, [...]

Shape and Appearance Models for Automatic Coronary Artery Tracking
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Automatic tracking of coronary arteries in Computed Tomography Angiography (CTA) is a challenging task. To accomplish it we propose a method consisting of two main steps: (1) A 3D model of the heart is matched for detecting the approximate position of the [...]

An Automatic Segmentation of T2-FLAIR Multiple Sclerosis Lesions
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Multiple sclerosis diagnosis and patient follow-up can be helped by an evaluation of the lesion load in MRI sequences. A lot of automatic methods to segment these lesions are available in the literature. The MICCAI workshop Multiple Sclerosis (MS) lesion [...]

Automatic Segmentation of MS Lesions Using a Contextual Model for the MICCAI Grand Challenge
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Automatically segmenting subcortical structures in brain images has the potential to greatly accelerate drug trials and population studies of disease. Here we propose an automatic subcortical segmentation algorithm using the auto context model. Unlike many [...]

Cognition Network Technology for a Fully Automated 3D Segmentation of Liver Tumors
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The Definiens Cognition Network Technology is applied to detect automatically tumors in a human liver. On the basis of a test data set containing ten tumors we show first quantitative results which are compared to manual segmentations provided by medical [...]

Head and Neck Auto-segmentation Challenge
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This paper presents the results of the Head and Neck Auto-segmentationChallenge, which was part of the workshop “3D Segmentation in the Clinic: A Grand Challenge”. This workshop took place in London, UK, in September 2009, in conjunction with the 12th [...]

Biomarker Detection in Whole Slide Imaging based on Statistical Color Models
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This paper presents a technique for immunostaining biomarker detection in digital slides. We treat immunostaining detection as a color image analysis problem and build statistical color models using a large number of labeled positive and negative [...]

Escher's Ants as Metaphor:   Topological Marching for the Well-Composed, Genus Zero Crowd
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Topological considerations for segmentation results are important for such applications as proper brain segmentation from digital image data. We present an enhancement of the FastMarchingImageFilter which allows for topologically constrained evolution of the [...]

4D Morphological segmentation and the MICCAI LV-segmentation grand challenge
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The goal of the Cardiac MR Left Ventricle Segmentation Challenge at MICCAI 2009 is to compare state-of-the-art LV segmentation methods. This goal is facilitated through an evaluation system and a database of cardiac cine MR images, as well as expert contours, [...]

OpenITGLinkMUSiiC: A Standard Communications Protocol for Advanced Ultrasound Research
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Ultrasound imaging is the most popular and safe diagnostic medical imaging modality. Over the past years, a considerable number of studies have been conducted on new medical ultrasound imaging modalities such as ultrasound-based elasticity imaging, [...]

Simulated Diffusion-Weighted Imaging for the ITK Masses
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A recent article by Van Hecke et al. [3] describes a framework for creating simulated diffusion-weighted images (DWI). The methodology allows for modeling intersubject variability, regional pathology, and noise and is quite useful for evaluation purposes. [...]

Exporting Contours to DICOM-RT Structure Set
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This paper presents an ITK implementation for exporting the contours of the automated segmentation results to DICOM-RT Structure Set format. The “radiotherapy structure set” (RTSTRUCT) object of the DICOM standard is used for the transfer of patient [...]

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 [...]

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 [...]

Performance Benchmarking the Insight Toolkit
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This document describes a module for the Insight Toolkit (ITK) to assist in performance benchmarking and a suite of benchmarks for the toolkit. These resources provide metrics to quantify software computational performance. This is a pre-requisite to improve [...]

Graph Cuts, <i>Caveat Utilitor</i>, and Euler's Bridges of Konigsberg
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Graph-based algorithms have enjoyed renewed interest for solving computer vision problems. These algorithms have been the subject of intense interest and research. In order to maintain the ITK library au courant, we developed a framework for graph-based [...]

Computing Textural Feature Maps for N-Dimensional images
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This document describes a new remote module implemented for the Insight Toolkit ITK, itkTextureFeatures. This module contains two texture analysis filters that are used to compute feature maps of N-Dimensional images using two well-known texture analysis [...]

User-Guided Level Set Segmentation of Anatomical Structures with ITK-SNAP
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Active contour segmentation and its robust implementation using level sets have been studied thoroughly in the medical image analysis literature. Despite the availability of these powerful methods, clinical research still largely relies on manual [...]

A Framework for Algorithm Evaluation and Clinical Application Prototyping using ITK
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The usage of image processing has become an important and continuous growing field in medical imaging. Although a large amount of algorithms is available, only few are routinely applied within applications for clinical diagnosis support and treatment [...]

A role-based component architecture for computer assisted interventions: illustration for electromagnetic tracking and robotized motion rejection in flexible endoscopy
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This paper presents an original role-based software architecture facilitating the flexible composition, configuration and collaboration of separated components in the field of computer assisted interventions. Roles, which can be seen as methods dynamically [...]

Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM
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Shape analysis has become of increasing interest to the neuroimaging community due to its potential to precisely locate morphological changes between healthy and pathological structures. This manuscript presents a comprehensive set of tools for the [...]

Nearly automatic vessels segmentation using graph-based energy minimization
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We present a nearly automatic tool for the accurate segmentation of vascular structures in volumetric CTA images. Its inputs are a start and an end seed points inside the vessel. The two-step graph-based energy minimization method starts by computing the [...]

Leveraging Open Source for Geographically Dispersed Workflows
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Personalized simulations can help assess and predict the clinical status of patients and are a key tenet of the Virtual Physiological Human (VPH) framework. This paper shows how the turnkey access of GIMIAS, an open source software platform built on open [...]

Connected Component and Morphology Based Extraction of Arterial Centerlines of the Heart (CocomoBeach)
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This document describes a novel scheme for the automated extraction of the central lumen lines of coronary arteries from computed tomography angiography (CTA) data. The scheme first obtains a seg- mentation of the whole coronary tree and subsequently [...]

Multi-Atlas-based Segmentation with Hierarchical Max-Flow
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This study investigates a method for brain tissue segmentation from 3D T1 weighted (T1w) MR images via convex relaxation with a hierarchical ordering constraint. It employs a multi-atlas-based initialization from 5 training images and is tested on 12 T1w MR [...]

Image registration using the Morphon algorithm: an ITK implementation
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Medical image registration is becoming a more and more useful component of a large number of applications. The presented method aims to enrich the ITK library. This method, called Morphon registration algorithm, computes a dense deformation field accepting [...]

Transitively Consistent and Unbiased Multi-Image Registration using Numerically Stable Transformation Synchronisation
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Transitive consistency of pairwise transformations is a desirable property of groupwise image registration procedures. The transformation synchronisation method (Bernard et al., 2015) is able to retrieve transitively consistent pairwise transformations from [...]

An Open Source Framework for Surgical Simulation
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In this work a software framework for the virtual surgical simulation is presented. Our environment ESQUI (The acronym comes from the Spanish "Entorno para Simulacion QUIrurgica", i.e. Framework for Surgical Simulation) is based on an open software and [...]

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 [...]

ITK-based Registration of Large Images from Light Microscopy: A Biomedical Application
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Inactivation of the retinoblastoma gene in mouse embryos results in morphological changes in the placenta, which has been shown to affect fetal survivability. The construction of a 3D virtual placenta aids in accurately quantifying structural changes [...]

Clustering Based Cardiac Resynchronization Therapy Prediction using Open Source Toolkit PRTools
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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 [...]

Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems
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This document describes work-in-progress for refactoring ITK’s registration methods to exploit the parallel, computation power of multi-processor, shared-memory systems. Refactoring includes making the methods multi-threaded as well as optimizing the [...]

Fast BlockMatching Registration with Entropy-based Similarity
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This paper describes the implementation of a multidimensional block-matching nonrigid registration algorithm. The main features of the algorithm are its simplicity, its free form nature, the modularity of the similarity measure, which makes it possible [...]

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 [...]

Coupling Finite Element and Mesh-free Methods for Modelling Brain Deformation in Response to Tumour Growth
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Very little is known about the deformation effects of tumour growth within the brain. Computer simulations have the potential to calculate such deformations. A method for computing localised high deformations within the brain's soft tissue is presented. [...]

Segmentation of Liver Metastases in CT Scans by Adaptive Thresholding and Morphological Processing
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This article presents an algorithm for the segmentation of liver metastases in CT scans. It is a hybrid method that combines adaptive thresholding based on a gray value analysis of the ROI with model-based morphological processing. We show the results of the [...]

On What Manifold do Diffusion Tensors Live?
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Diffusion tensor imaging has become an important research and clinical tool, owing to its unique ability to infer microstructural properties of living tissue. Increased use has led to a demand for statistical tools to analyze diffusion tensor data and [...]

Meeting Andy Warhol Somewhere Over the Rainbow:  RGB Colormapping and ITK
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Although greyscale intensity values are primarily used in image data visualization oftentimes, due to the requirements of aesthetics (whether they be self-imposed or collaborator-suggested), mapping the greyscale image to a user-defined colormap is desired. [...]

An iterative Bayesian approach for liver analysis: tumors validation study
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We present a new method for the simultaneous, nearly automatic segmentation of liver contours, vessels, and tumors from abdominal CTA scans. The method repeatedly applies multi-resolution, multi-class smoothed Bayesian classification followed by [...]

A VTK-based, CUDA-optimized Non-Parametric Vessel Detection Method
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We present a VTK-based implementation of our non-parametric vessel detection method that identifies vascular structures using a polar neighborhood profile. To accelerate the computationally intensive parts of the algorithm, we leverage the hardware [...]

Flexible architecture and modularity requirements for image guided cardiovascular surgeries
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Research and development of image guided surgery techniques requires software that provides a high degree of flexibility, with easy access to reliable functionality for common tasks. The goal of this paper is to highlight this claim in the context of image [...]

An Integrated Computer-Aided Robotic System for Dental Implantation
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This paper describes an integrated system for dental implantation including both preoperative planning utilizing computer-aided technology and automatic robot operation during the intra-operative stage. A novel two-step registration procedure was applied for [...]

LV Challenge LKEB Contribution: Fully Automated Myocardial Contour Detection
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In this paper a contour detection method is described and evaluated on the evaluation data sets of the Cardiac MR Left Ventricle Segmentation Challenge as part of MICCAI 2009’s 3D Segmentation Challenge for Clinical Applications. The proposed method, using [...]

Small Computings for Clinicals and SCCToolKit, OR friendly Trial Package and Software Development Kit
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This paper is about a design policy for operation-room (OR) friendly research system, software and a software toolkit SCCToolKit for this purpose, and a few examples. Examples are image processor for endoscope, OR event detector, vision based registration of [...]

Importing Contours from DICOM-RT Structure Sets
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This paper presents parsing software for importing contours from DICOM RT structure set files into binary image files. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image [...]

An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images
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Ultrasound has become a very important modality in image-guided therapy. At present, however, the collection, synchronization and transfer of ultrasonic images are more cumbersome than necessary. This paper presents a reusable solution to these problems. We [...]

Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching
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We present a novel method for segmentation and tracking of the left ventricle (LV) in 4D ultrasound sequences using a combination of automatic segmentation at the end-diastolic frame and tracking using both a global optical flow-based tracker and local block [...]

Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images
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As part of the CETUS challenge, we present a multi-atlas segmentation framework to delineate the left-ventricle endocardium in echocardiographic images. To increase the robustness of the registration step, we introduce a speckle reduction step and a new shape [...]

Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests
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In this paper, we present the use of a generic image segmentation method, namely a succession of Random Forest classifiers in an autocontext framework, for the MICCAI 2014 Challenge on Endocardial 3D Ultrasound Segmentation (CETUS). The proposed method [...]

Enabling ITK-based processing and 3D Slicer MRML scene management in ParaView
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This paper documents on-going work to facilitate ITK-based processing and 3D Slicer scene management in ParaView. We believe this will broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The [...]

MR Brain Segmentation using Decision Trees
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Segmentation of the human cerebrum from magnetic resonance images (MRI) into its component tissues has been a defining problem in medical imaging. Until recently, this has been solved as the tissue classification of the T1-weighted (T1-w) MRI, with numerous [...]

GPU and CPU implementation of Young - Van Vliet's Recursive Gaussian Smoothing Filter
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This document describes an implementation for GPU and CPU of Young and Van Vliet's recursive Gaussian smoothing as an external module for the Insight Toolkit ITK, version 4.* www.itk.org. In the absence of an OpenCL-capable platform, the code will run the CPU [...]

A Flexible Variational Registration Framework
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In this article, we present an implementation of a flexible framework for non-parametric variational image registration, realized as part of ITK's finite difference solver hierarchy. In a variational registration setting, the transformation is found by [...]

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

A semi-automated method for liver tumor segmentation based on 2D region growing with
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Liver tumour segmentation from computed tomography (CT) scans is a challenging task. A semi-automatic method based on 2D region growing with knowledge-based constraints is proposed to segment lesions from constituent 2D slices obtained from 3D CT images. [...]

Semi-automatic Segmentation of Liver Tumors from CT Scans Using Bayesian Rule-based 3D Region Growing
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Automatic segmentation of liver tumorous regions often fails due to high noise and large variance of tumors. In this work, a semi-automatic algorithm is proposed to segment liver tumors from computed tomography (CT) images. To cope with the variance of [...]

Semi-automatic Segmentation of 3D Liver Tumors from CT Scans Using Voxel Classification and Propagational Learning
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A semi-automatic scheme was developed for the segmentation of 3D liver tumors from computed tomography (CT) images. First a support vector machine (SVM) classifier was trained to extract tumor region from one single 2D slice in the intermediate part of a [...]

Carotid Lumen Segmentation and Stenosis Grading Challenge
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This paper describes the Carotid Lumen Segmentation and Stenosis Grading Challenge, which was part of the workshop ``3D Segmentation in the Clinic: A Grand Challenge''. This workshop was part of the 12th conference on Medical Image Computing and Computer [...]

Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS)
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Real-time 3D echocardiography has already been shown to be an accurate tool for left ventricular (LV) volume assessment. However, LV border identification remains a challenging task, mainly because of the low contrast of the images combined with drop-out [...]

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 [...]

Collaborative Development of an open framework for medical simulation
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This paper investigates an Open Framework for Medical Simulation (named SOFA for Simulation Open Framework Architecture), and proposes ideas for structuring and supporting its expansion. Lately, through a joint effort between the Sim Group at CIMIT and the [...]

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 [...]

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) [...]

Cardiac motion estimation using multi-scale feature points
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Heart illnesses influence the functioning of the cardiac muscle and are the major causes of death in the world. Optic flow methods are essential tools to assess and quantify the contraction of the cardiac walls, but are hampered by the aperture problem. [...]

3D Segmentation In The Clinic: A Grand Challenge II at MICCAI 2008 - MS Lesion Segmentation
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This document examines the application of a new parametric method on the segmentation of MS lesions in brain sMRI, as applied to the data provided for the MS Lesion Segmentation Challenge at MICCAI 2008. The method uses the vector image joint histogram, [...]

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 [...]

Framework of US-guided therapeutic HIFU system for renal diseases
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The authors describe a framework for the US-guided therapeutic HIFU system for renal diseases. In particular, the HIFU system is integrated with robotic servoing capability so as to track quasi-periodically moving renal tumors and stones. The system is [...]

Active Contour-Based Segmentation of Head and Neck with Adaptive Atlas Selection
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This paper presents automated segmentation of structures in the Head and Neck (H&N) region, using an active contour-based joint registration and segmentation model. A new atlas selection strategy is also used. Segmentation is performed based on the dense [...]

Adaptations of MARACAS algorithm to the segmentation of the carotid bifurcation and stenosis quantification in CTA images
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This paper describes a 3D CTA image segmentation method submitted to the CLS09 contest (Carotid Lumen Segmentation and Stenosis Quantification) held in conjunction with the MICCAI 2009 conference. First, images are denoised to improve image quality and [...]

3D Slicer Based Surgical Robot Console System
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This document describes the surgical robot console system based on 3D Slicer for image-guided surgery. Considering the image-guided surgery, since image workstations have complex User Interface (UI) and extra functions, it is supposed that such UI is not [...]

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 [...]

Robot assisted prostate surgery using augmented reality with deformable models
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We present preliminary results of our work to develop an augmented display for improved visualization of the prostate and surrounding critical anatomy for robot-assisted prostate surgery. Prostate cancer is the second leading cause of cancer-related deaths in [...]

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 [...]

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 [...]

Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models
No opinion
Segmentation of 3D echocardiograms (3DEs) is still a challenging task due to the low signal-to-noise ratio, the limited field of view, and typical ultrasound artifacts. We propose to segment the left ventricular endocardial surface by using Active Appearance [...]

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 [...]

A patch-based framework for new ITK functionality: Joint fusion, denoising, and non-local super-resolution
No opinion
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 [...]

InsightToolkit Kinetic Analysis (itk::ka) Library
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This paper describes how to compile and use the Insight Toolkit Kinetic Analysis library (itk::ka), to perform analysis of dynamic medical images, along with a brief overview of the library source code. Supplied, are a set of interfaces to facilitate [...]

Evaluation Framework for Algorithms Segmenting Short Axis Cardiac MRI.
No opinion
The motivation of the segmentation challenge is to quantitatively analyze global and regional cardiac function from cine magnetic resonance (MR) images, clinical parameters such as ejection fraction (EF), left ventricle myocardium mass (MM), and stroke volume [...]

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

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 [...]

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 [...]

Coronary centerline tracking in CT images with use of an elastic model and image moments.
No opinion
This coronary-artery extraction method uses one initialization point per vessel. First, a mask is computed by use of a region-growing algorithm, which starts from the initial point and stops when no more connected voxels fall within an interactively defined [...]

3D Segmentation in the Clinic: A Grand  Challenge II: MS lesion segmentation
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This paper describes the setup of a segmentation competition for the automatic extraction of Multiple Sclerosis (MS) lesions from brain Magnetic Resonance Imaging (MRI) data. This competition is one of three competitions that make up a comparison workshop at [...]

Tensor Spectral Matching of Diffusion Weighted Images
No opinion
Very preterm birth coincides with a period of major development in the brain, with striking changes in volume, cortex folding and significant change at the microstructural level. Diffusion MRI is sensitive to motion of water on the scale of microns, allowing [...]

Segmentation of the Left Ventricle from Cine MR Images Using a Comprehensive Approach
No opinion
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 [...]


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ISSN 2327-770X
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