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Confidence Connected Segmentation of the Lateral Ventricles
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In this paper we attempt to segment the lateral ventricles using the ITK provided Confidence Connected algorithm. An ITK application was used to explore the various input parameters to produce an image of acceptable presentation. Input MRI data of healthy [...]

Reproducible Ventricle Segmentation Using Insight Toolkit
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This technical report describes how to use Insight Toolkit to perform elementary ventricle segmentation on data from the Designed Database of MR Brain Images of Healthy Volunteers hosted at MIDAS.

Open Source Software in the Development and Testing of an Image-Guided Robot System
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This paper describes the use of open source software in the development and testing of an image-guided robot system for small animal research, presented at MICCAI 2006. This system relied on a significant amount of open source software, including 3D [...]

Inverse Nonlinear Finite Element Methods for Surgery Simulation and Image Guidance
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Nonlinear finite element methods are described in which cyclic organ motion is implied from 4D scan data. The equations of motion corresponding to an explicit integration of the total Lagrangian formulation are reversed, such that the sequence of node forces [...]

Isotropic and Steerable Wavelets in N Dimensions. A multiresolution analysis framework.
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This document describes the implementation of the external module ITKIsotropicWavelets, a multiresolution (MRA) analysis framework using isotropic and steerable wavelets in the frequency domain. This framework provides the backbone for state of the art [...]

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 [...]

A Treatment Planning System for the Small Animal Radiation Research Platform (SARRP) based on 3D Slicer
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This paper describes the software integration of a treatment planning system (TPS), based on the open-source 3D Slicer package, with the Small Animal Radiation Research Platform (SARRP).The TPS is designed to enable researchers to replicate their clinical [...]

Parallel algorithms for erosion and dilation of label images.
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It is sometimes useful to be able to apply binary morphological operations, such as erosions and dilations, to labelled images in a fashion that preserves the labels. This article introduces a specialised class implementing parallel methods described in beare [...]

Total Quality Management in Healthcare
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This paper presents the description on Healthcare organizations are required to focus on Total quality improve:- Rendering acceptable, quality health services to patients at affordable price within reasonable price, within in a reasonable time; Applying zero [...]

VV: a viewer for the evaluation of 4D image registration
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We propose an open source and cross platform medical image viewer, named VV, designed for qualita tive evaluation of images registration, in particular for deformable registration of 4D CT images. VV can display multiple spatio-temporal image sequences (2D+t [...]

Computational Biomechanics for Medicine III - Workshop proceedings
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A novel partnership between surgeons and machines, made possible by advances in computing and engineering technology, could overcome many of the limitations of traditional surgery. By extending surgeons' ability to plan and carry out surgical interventions [...]

Computational Biomechanics for Medicine III: a MICCAI 2008 satellite
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Mathematical modeling and computer simulation have proved tremendously successful in engineering. One of the greatest challenges for mechanists is to extend the success of computational mechanics to fields outside traditional engineering, in particular to [...]

VascuSynth: Vascular Tree Synthesis Software
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In previous work, we presented an algorithm to synthesize volumetric images of vascular trees and generate the corresponding ground truth segmentations, bifurcation locations, branch properties, and tree hierarchy. In this work, we provide the software needed [...]

A novel atlas-selection approach for multi-atlas based segmentation using the correlation of inter-atlas similarities
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Automated segmentation is a frequently applied task in the course of medical imaging. Furthermore, it is a substantial component of image-guided radiotherapy. Atlas based segmentation is one of the most frequently used approach for automated segmentation. [...]

Fast image-based model of mitral valve closure for surgical planning
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Surgical repair of the mitral valve results in better outcomes than valve replacement, yet diseased valves are often replaced due to the technical difficulty of the repair process. A surgical planning system based on patient-specific medical images that [...]

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 [...]

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 [...]

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 [...]

Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut
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In this paper, we present a fast and interactive graph cut method for 3D segmentation of the endocardial wall of the left ventricle (LV) given 3D echocardiographic images. This is a challenging task due to the poor contrast and the low signal-to-noise ratio [...]

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 [...]

GeoInterp: Contour Interpolation with Geodesic Snakes
Geodesic Snakes
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The process of outlining organs on three dimensional medical images is extremely time-consuming. In this document, we describe a new tool that can interpolate contours and also make them smooth. The tool uses geodesic snakes to perform these functions. The [...]

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

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 [...]

vtkINRIA3D: A VTK Extension for Spatiotemporal Data Synchronization, Visualization and Management
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This paper presents an extension of the Visualization ToolKit dedicated to spatiotemporal data synchronization, visualization and management. It basically consists in a versatile library providing functionalities to help developers setting up sophisticated [...]

A White Matter Stochastic Tractography System
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White matter tractography enables studies of fiber bundle characteristics. Stochastic tractography facilitates these investigations by providing a measure of confidence regarding the inferred fiber bundles. This article presents a multithreaded ITK [...]

Systems and Architectures for Computer-Assisted Interventions
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The goal of this workshop is to establish a forum for discussing open source toolkits and open interfaces and how they have been applied in the development of computer assisted intervention systems. The intent is to establish a dialogue between the open [...]

The MUSiiC Toolkit: Modular Real-Time Toolkit for Advanced Ultrasound Research
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Ultrasound is a very useful and convenient modality in medical imaging, due to its relatively small footprint, high resolution, negligible adverse effects, and real-time imaging capability -- in spite of its well-known artifacts. However, it is fairly [...]

Uniform B-Splines for the VTK Imaging Pipeline
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Uniform B-splines are used widely in image processing because they provide maximal smoothness compared to any other piecewise polynomial of the same degree and support. This paper describes VTK classes for performing two functions: image interpolation via [...]

EM Segmentation: Automatic Tissue Class Intensity Initialization Using K-means
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ABSTRACT Brain tissue segmentation is important in many medical image applications. We augmented the Expectation-Maximization segmentation algorithm in Slicer3 (www.spl.harvard.edu) . Currently, in the EM Segmenter module in Slicer3 user input is necessary to [...]

Open Topology: A Toolkit for Brain Isosurface Correction
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Isosurface extraction from brain images often creates handles between brain folds that are anatomically separated. Although manual editing could optimally correct these anatomical errors, it is not realistic due the size of the 3D data and the convoluted [...]

Automated Walks using Machine Learning for Segmentation
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This paper describes an automated algorithm for segmentation of brain structures (CSF, white matter, and gray matter) in MR images. We employ machine learning, i.e. k-Nearest Neighbors, of features derived from k-means, Canny edge detection, and Tourist [...]

An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects
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An Insight Toolkit (ITK) algorithm for detection of spherical objects using Hough methods with voting is presented in this paper. Currently, the usage of Hough methods for detecting linear and circular elements exists for 2D images in ITK. The current work [...]

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 [...]

Non-rigid Groupwise Registration using B-Spline Deformation Model
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In this work, we extend a previously demonstrated entropy based groupwise registration method to include a non-rigid deformation model based on B-splines. We describe an open source implementation of the groupwise registration algorithm using the [...]

Multidimensional Arrays and the nArray Package
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At the Johns Hopkins University’s Engineering Research Center for Computer-Integrated Surgical Systems and Technology (ERC-CISST) laboratory, we have designed and developed a platformindependent C++ software package, called the nArray library, that provides [...]

On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands
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The segmentation of parotid glands in CT scans of patients with head and neck cancer is an essential part of treatment planning. We introduce a new method for the automatic segmentation of parotid glands that extends existing patch-based approaches in three [...]

Modified Expectation Maximization Method for Automatic Segmentation of MR Brain Images
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An automated method of MR Brain image segmentation is presented. A block based Expectation Maximization method is presented for the tissue classification of MR Brain images. The standard Gaussian Mixture Model is the most widely used method for MR Brain Image [...]

Multiple Sclerosis Lesion Segmentation Using Statistical and Topological Atlases
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This paper presents a new fully automatic method for segmentation of brain images that possess multiple sclerosis (MS) lesions. Multichannel magnetic resonance images are used to delineate multiple sclerosis lesions while segmenting the brain into its [...]

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 [...]

The cisst libraries for computer assisted intervention systems
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Computer assisted intervention (CAI) systems require the integration of an increasing number of devices, including medical monitors, sensors, tracking devices and robots. This complexity makes applications harder to develop, more difficult to debug and the [...]

Automated MS-Lesion Segmentation by K-Nearest Neighbor Classification
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This paper proposes a new method for fully automated multiple sclerosis (MS) lesion segmentation in cranial magnetic resonance (MR) imaging. The algorithm uses the T1-weighted and the fluid attenuation inversion recovery scans. It is based the K-Nearest [...]

Segmenting the Left Ventricle in 3D Using a Coupled ASM and a Learned Non-Rigid Spatial Model
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This paper presents a new approach to higher dimensional segmentation. We present an extended Active Shape Model (ASM) formulation for the segmentation of multi-contour anatomical structures. We employ coupling and weighting schemes to improve the robustness [...]

Iterative Smoothing of Field Data in Spherical Meshes
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This document describes a contribution to the Insight Toolkit intended to smooth the values of Field data associated with the nodes of a Spherical Mesh. The Mesh Smoothing filters contributed here do not modify the geometry or the topology of the Mesh. They [...]

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 [...]

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 [...]

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. [...]

Radial Thickness Calculation and Visualization for Volumetric Layers
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Volumetric layers often encountered in medical image analysis are characterized by double and nested bounding surfaces. The thickness of a volumetric layer at a point on the bounding surface is the distance from that point to the opposite surface. There exist [...]

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 [...]

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 [...]

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 [...]

Visual Programming of VTK Pipelines in Simulink
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We have created a wrapper package named SimVTK that allows VTK, and third-party classes derived from VTK classes, to be seamlessly integrated with MATLAB's Simulink interface. Our package generates a loadable Simulink module for each VTK class, which is then [...]

An Open-Source Hardware and Software Platform for Telesurgical Robotics Research
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We present our work to develop a telerobotics research platform that provides complete access to all levels of control via open-source custom electronics and software. The electronics employs an FPGA to enable a centralized computation and distributed I/O [...]

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 [...]

Integration of the Java Image Science Toolkit with E-Science Platform
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Medical image analyses rely on diverse software packages assembled into a “pipeline”. The Java Image Science Toolkit (JIST) has served as a standalone plugin into the Medical Image Processing Analysis and Visualization (MIPAV). We addressed shortcomings [...]

Rotational Registration of Spherical Surfaces Represented as QuadEdge Meshes
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This document describes a contribution to the Insight Toolkit intended to support the process of registering two Meshes. The methods included here are restricted to Meshes with a Spherical geometry and topology, and with scalar values associated to their [...]

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 [...]

Development of open source software for computer-assisted intervention systems
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We are developing open source software for computer assisted intervention systems. Our primary experience has been with medical robots, but the concepts (and software) apply to many physical devices that interact with the real world. The real-time [...]

Simulation of Active Cardiac Dynamics with Orthotropic Hyperelastic Material Model
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Meaningful physical models are important for studying cardiac physiology, such as quantitative assessments of pathology via changes in model parameters, and recovering information from medical images. In order to achieve realistic deformation studies, an [...]

Nonlinear Elastic Registration with Unbiased Regularization in Three Dimensions
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We propose a new nonlinear image registration model which is based on nonlinear elastic regularization and unbiased registration. The nonlinear elastic and the unbiased regularization terms are simplified using the change of variables by introducing an [...]

A robust Expectation-Maximization algorithm for Multiple Sclerosis lesion segmentation
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A fully automatic workflow for Multiple Sclerosis (MS) lesion segmentation is described. Fully automatic means that no user interaction is performed in any of the steps and that all parameters are fixed for all the images processed in beforehand. Our workflow [...]

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 [...]

Segmentation of Liver Metastases Using a Level Set Method with Spiral-Scanning Technique and Supervised Fuzzy Pixel Classification
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In this paper a specific method is presented to facilitate the semi-automatic segmentation of liver metastases in CT images. Accurate and reliable segmentation of tumors is e.g. essential for the follow-up of cancer treatment. The core of the algorithm is a [...]

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. [...]

Spherical Demons Registration of Spherical Surfaces
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As demonstrated by the example videos accompanying this submission of the multiresolution implementation of Spherical Demons, the registration appears reasonable. However, we are still unable to replicate the warps from the stable and well verified [...]

Automatic Image-Driven Segmentation of Left  Ventricle in Cardiac Cine MRI
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This study investigates a fully automatic left ventricle segmentation method from cine short axis MR images. Advantages of this method include that it: 1) is image-driven and does not require manually drawn initial contours. 2) provides not only endocardial [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

Camino: Diffusion MRI reconstruction and processing
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Camino is an open-source, object-oriented software package for processing diffusion MRI data. Camino implements a data processing pipeline, which allows for easy scripting and flexible integration with other software. This paper summarises the features of [...]

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 [...]

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) [...]

Assessment of Peri-Articular Implant Fitting Based on Statistical Finite Element Modeling
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We present a framework for statistical finite element analysis allowing performing statistical statements of biomechanical performance of peri-articular implants across a given population. In this paper, we focus on the design of orthopaedic implants that fit [...]

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, [...]

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 [...]

A Surgical Assistant Workstation (SAW) Application for Teleoperated Surgical Robot System
No opinion
The Surgical Assistant Workstation (SAW) modular software framework provides integrated support for robotic devices, imaging sensors, and a visualization pipeline for rapid prototyping of telesurgical research systems. Subsystems of a telesurgical system, [...]

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 [...]

Component-based software for dynamic configuration and control of computer assisted intervention systems
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This paper presents the rationale for the use of a component-based architecture for computer-assisted intervention (CAI) systems, including the ability to reuse components and to easily develop distributed systems. We introduce three additional capabilities, [...]

Prototyping a Hybrid Cooperative and Tele-robotic Surgical System for Retinal Microsurgery
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This paper presents the design of a tele-robotic microsurgical platform designed for development of cooperative and tele-operative control schemes, sensor based smart instruments, user interfaces and new surgical techniques with eye surgery as the driving [...]

CITK - an architecture and examples of CUDA enabled ITK filters
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There is great interest in the use of graphics processing units (GPU)for general purpose applications because the highly parallel architectures used in GPUs offer the potential for huge performance increases. The use of GPUs in image analysis applications has [...]

Evaluation Framework for Algorithms Segmenting Short Axis Cardiac MRI.
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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: 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 [...]

The Surgical Assistant Workstation (SAW) in Minimally-Invasive Surgery and Microsurgery
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The Surgical Assistant Workstation (SAW) provides a modular, open-source software framework to support rapid prototyping of computer-assisted surgery systems, especially those that benefit from enhanced 3D visualization and user interaction. The framework [...]

Coronary centerline tracking in CT images with use of an elastic model and image moments.
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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 [...]


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