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Automatic Coronary Tree Modeling
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In this paper, we present an automatic method for extracting center axis representations (centerlines) of coronary arteries in contrast enhanced (CE)-CT angiography scans. The algorithm first detects the aorta which is used as an initial mask for [...]

Coronary Artery Centerline Tracking Using Axial Symmetries
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We present a method for tracking a coronary artery centerline given a single user supplied distal endpoint. Briefly, we first isolate the aorta and compute its surface. Next, we apply a novel two-stage Hough-like election scheme to the image volume to detect [...]

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 [...]

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.

Fully Automatic Segmentation of Head and Neck Organs using Active Appearance Models
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We present a fully automatic model based system for segmenting the mandible, parotid and submandibular glands, brainstem, optic nerves and the optic chiasm in CT images, which won the MICCAI 2015 Head and Neck Auto Segmentation Grand Challenge. The method is [...]

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 [...]

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 [...]

Confidence connected segmentation
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This document describes a tiny application developed using the Insight Toolkit, ITK www.itk.org. The goal of the document is to facilitate ease of use of the application by following the guidelines given in the document. The application does not claim to [...]

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 [...]

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 [...]

Graph Cuts Based Super Pixel Segmentation for VTK
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Segmenting images into "super pixels" is lately a very hot topic. One implementation of such a technique is by Felzenszwalb and Huttenlocher. We propose a new class, vtkSuperPixelSegmentation, which has wrapped Felzenszwalb's code (with permission) to provide [...]

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

Interactive Image Graph Cut Segmentation
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This document presents a system to "scribble" on an image to mark foreground and background pixels and then feed these pixels to a graph cuts segmentation technique. The interaction is done using the Visualization Toolkit and the processing is done using the [...]

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 [...]

The watershed transform in ITK - discussion and new developments
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This report discusses various definitions and implementations of the watershed transform as well as providing an introduction to some well known techniques for applying the watershed transform to practical problems. The discussion will be focused on new and [...]

Robot Assisted Needle Placement: Application developed using an open source image guided surgery toolkit (IGSTK)
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Using a robot system to position needles or needle shaped tools during clinical procedures such as biopsy, radio frequency ablation, and target drug delivery has a great potentials in increasing accuracy and speed of the process, and minimizing trauma to [...]

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 Modification to Otsu Thresholding Method for ICV Segmentation
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A modification is made to Otsu thresholding method. It provides better results for ICV (Intracranial volume) segmentation on one kind of T2-weighted MRI data.

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

Connected Threshold Segmentation of Ventricles in the Brain
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This document describes an implementation of Connected Threshold Segmentation to isolate the ventricles using Insight Toolkit www.itk.org.

Experimenting with Segmentation in ITK
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This document describes some experiments for segmentation using the Insight Toolkit ITK url{www.itk.org}. The code of the experiment is written following the ITK CodingStyle as described in the directory [...]

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 [...]

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 [...]

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 [...]

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 [...]

Clustering Segmentation for VTK
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This document presents a VTK implementation of the algorithm described in "A clustering method for efficient segmentation of 3D laser data" by Klasing, Klaas Wollherr, Dirk, and Buss, Martin. The algorithm . The code is available [...]

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

Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models
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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 [...]

Model-based left ventricle segmentation in 3D ultrasound using phase image
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In this paper, we propose a semi-automatic method for left ventricle segmentation. The proposed method utilizes a multi-scale quadrature filter method to enhance the 3D volume, followed by a model-based level set method to segment the endocardial surface of [...]

Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates
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A method for real-time automatic tracking of the left ventricle (LV) in 3D ultrasound is presented. A mesh model of the LV is deformed using mean value coordinates enabling large variations. Kalman filtering and edge detection is used to track the mesh in [...]

Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors
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We propose a learning based approach to perform automatic segmentation of the left ventricle in 3D cardiac ultrasound images. The segmentation contour is estimated through the use of a variant of Hough forests whose object localization capabilities are [...]

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 [...]

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 [...]

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 [...]

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

Multi-object Segmentation of Head Bones
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We present a fully automatic method for 3D segmentation of the mandibular bone from CT data. The method includes an adaptation of statistical shape models of the mandible, the skull base and the midfacial bones, followed by a simultaneous graph-based [...]

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

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 [...]

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 [...]

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 [...]

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 [...]

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. [...]

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 [...]

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 [...]

Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours
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An Insight Toolkit (ITK) processing framework for blob segmentation with applications to microscopy images is presented in this paper. Our algorithm is a refinement of the work of Mosaliganti et al. [3] for splitting cell clusters. The basic idea is to [...]

Implementation of graph-based interactive 3D vessel segmentation filter
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This paper describes an ITK implementation of a 3D vascular segmentation filter using a graph-based energy minimization algorithm. The method first computes the shortest path between two user provided points in the vessel and then performs a graph min-cut [...]

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 [...]

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 [...]

Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes
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An Insight Toolkit (ITK) processing framework for segmenting and tracking nuclei in time-lapse microscopy images using coupled active contours is presented in this paper. We implement the method of Dufour et al.[2] to segment and track cells in fluorescence [...]

Semi-automated cardiac segmentation on cine magnetic  resonance images using GVF-Snake deformable models
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The segmentation of left ventricular structures is necessary for the evaluation of the ejection fraction (EF) and the myocardial mass (LVM). A semi-automated 2D algorithm using connected filters and a deformable model allowing an accurate endocardial [...]

Fully Automatic Left Ventricle Segmentation in Cardiac Cine MR Images Using Registration and Minimum Surfaces
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This paper describes a fully automatic system to segment the left ventricle in all slices and all phases of a magnetic resonance cardiac cine study. After localizing the left ventricle blood pool using motion, thresholding and clustering, slices are [...]

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 [...]

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 [...]

Gauss-Newton Method for Segmentation assisted Deformable Registration
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In this work, we try to develop a fast converging method for segmentation assisted deformable registration. The segmentation step consists of a piece-wise constant Mumford-Shah energy model while reg- istration is driven by the sum of squared distances of [...]

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 [...]

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 [...]

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 [...]

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 [...]

Multimodal MR Brain Segmentation Using Bayesian-based Adaptive Mean-Shift (BAMS)
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In this paper, we validate our proposed segmentation algorithm called Bayesian-based adaptive mean-shift (BAMS) on real mul-timodal MR images provided by the MRBrainS challenge. BAMS is a fully automatic unsupervised segmentation algorithm. It is based on the [...]

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 [...]

Fast Marching Minimal Path Extraction in ITK
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This paper describes the ITK implementation of a minimal path extraction framework based on Fast Marching arrival functions. The method requires the user to provide three inputs: 1. a meaningful speed function to generate an arrival function, 2. path [...]

Fuzzy Clustering Algorithms for Image Segmentation
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In this document we present the implementation of three fuzzy clustering algorithms using the Insight Toolkit ITK. Firstly, we developed the conventional Fuzzy C-Means that will serve as the basis for the rest of the proposed algorithms. The next algorithms [...]

Automatic Segmentation of Structures in CT Head and Neck Images using a Coupled Shape Model
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The common approach to do a fully automatic segmentation of multiple structures is an atlas or multi-atlas based solution. These already have proven to be suitable for the segmentation of structures in the head and neck area and provide very accurate [...]

Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models
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A new patch based label fusion method based on generative approach is proposed for segmentation of mandible, brainstem, parotid and submandibular glands, optic nerves and the optic chiasm in head and neck CT images. The proposal constructs local classifiers [...]

Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models
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A new patch based label fusion method based on generative approach is proposed for segmentation of mandible, brainstem, parotid and submandibular glands, optic nerves and the optic chiasm in head and neck CT images. The proposal constructs local classifiers [...]

A nonparametric, entropy-minimizing MRI tissue classification algorithm implementation using ITK
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This paper focuses on the role of open-source software in the development of a novel magnetic resonance image (MRI) tissue classification algorithm. Specifically, we describe the of use existing classes in the Insight Segmentation and Registration Toolkit [...]

Segmentation of Skull-infiltrated Tumors Using ITK: Methods and Validation
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Methods for segmentation of skull infiltrated tumors in Computed Tomography (CT) images using Insight Segmentation and Registration Toolkit ITK (www.itk.org) are presented. Pipelines of filters and algorithms from ITK are validated on the basis of [...]

Automatic MS Lesion Segmentation by Outlier Detection and Information Theoretic Region Partitioning
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Multiple Sclerosis (MS) is a neurodegenerative disease that is associated with brain tissue damage primarily observed as white matter abnormalities such as lesions. We present a novel, fully automatic segmentation method for MS lesions in brain MRI that [...]

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, [...]

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 [...]

Implementation of weighted Dijkstra’s shortest-path algorithm for n-D images
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This paper describes the ITK implementation of a shortest path extraction algorithm based on graph representation of the image and the Dijkstra shortest path algorithm. The method requires the user to provide two inputs: 1. path information in the form of [...]

Carotid arteries segmentation in CT images with use of a right generalized cylinder model
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The arterial lumen is modeled by a spatially continuous right generalized cylinder with piece-wise constant parameters. The method is the identifies the parameters of each cylinder piece from a series of planar contours extracted along an approximate axis of [...]

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 [...]

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 [...]

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 [...]

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 [...]

Automated Brain-Tissue Segmentation by Multi-Feature SVM Classification
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We present a method for automated brain-tissue segmentation through voxelwise classification. Our algorithm uses manually labeled training images to train a support vector machine (SVM) classifier, which is then used for the segmentation of target images. The [...]

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

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 [...]

Gaussian Intensity Model with Neighborhood Cues for Fluid-Tissue Categorization of Multi-Sequence MR Brain Images
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This work presents an automatic brain MRI segmentation method which can classify brain voxels into one of three main tissue types: gray matter (GM), white matter (WM) and Cerebro-spinal Fluid (CSF). Intensity-model based classification of MR images has proven [...]

Fostering Open Science in Lung Cancer Lesion Sizing with ITK module LSTK
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This document describes the latest efforts in integrating the Lesion Sizing Toolkit (LSTK) into ITK v4 as an external/remote module providing an Open Science dashboard website with a large open image archive of lung cancer CT images for LSTK development and [...]

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

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

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 [...]

An Intelligent cluster-based segmentation using Wavelet Features:Application to Medical Images
No opinion
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 [...]

Automatic Segmentation of Head and Neck CT Images by GPU-Accelerated Multi-atlas Fusion
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Treatment planning for high precision radiotherapy of head and neck (H&N) cancer patients requires accurate delineation of critical structures. Manual contouring is tedious and often suffers from large inter- and intra-rater variability. In this paper, we [...]

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 [...]

Multi Atlas Segmentation with Active Shape Model Refinement for Multi-Organ Segmentation in Head and Neck Cancer Radiotherapy Planning
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We describe a segmentation method that was used in the Head and Neck Auto Segmentation Challenge held at the MICCAI 2015 conference. The algorithm consists of two building blocks. First, we employ a multi-atlas segmentation to obtain an initial segmentation [...]

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

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 [...]

Coronary Centerline Extraction Using Multiple Hypothesis Tracking and Minimal Paths
No opinion
This paper describes an interactive approach to the identification of coronary arteries in 3D angiography images. The approach is based on a novel multiple hypothesis tracking methodology which is complemented with a standard minimal path search, and it [...]

An Automatic Seeding Method For Coronary Artery Segmentation and Skeletonization in CTA
No opinion
An automatic seeding method for coronary artery segmentation and skeletonization is presented. The new method includes automatic removal of the rib cage, tracing of the ascending aorta and initial planting of seeds for the coronary arteries. The automatic [...]

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 [...]

Ensemble segmentation using AdaBoost with application to liver lesion extraction from a CT volume
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This paper describes an ensemble segmentation trained by the AdaBoost algorithm, which finds a sequence of weak hypotheses, each of which is appropriate for the distribution on training example, and combines the weak hypotheses by a weighted majority vote. In [...]

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 [...]

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 [...]

A Minimal Cost Path and Level Set Evolution Approach for Carotid Bifurcation Segmentation
No opinion
We propose a new approach for semi-automatic segmentation of the carotid bifurcation as part of the Carotid Lumen Segmentation and Stenosis Grading Challenge MICCAI'2009 workshop. Three initial points are provided as input, belonging to the Common, the [...]

New Expectation Maximization Segmentation Pipeline in Slicer 3
No opinion
Many neuroanatomy studies rely on brain tissue segmentation in Magnetic Resonance images (MRI). The Expectation-Maximization (EM) theory offers a popular framework for this task. We studied the EM algorithm developed at the Surgical Planning Laboratory (SPL) [...]

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 [...]

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 [...]

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, [...]

MAP–Based Framework for Segmentation of MR Brain Images Based on Visual Appearance and Prior Shape
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We propose a new MAP-based technique for the unsupervised segmentation of different brain structures (white matter, gray matter, etc.) from T1-weighted MR brain images. In this paper, we follow a procedure like most conventional approaches, in which [...]

A novel atlas-selection approach for multi-atlas based segmentation using the correlation of inter-atlas similarities
No opinion
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. [...]

Automatic Brain Tissue Segmentation of Multi-sequence MR Images Using Random Decision Forests
No opinion
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 [...]

I-DO: A Deformable Organisms framework for ITK
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Medical image analysis is an important problem relating to the study of various diseases. Since their inception to MICCAI in 2001, ''deformable organisms'' have emerged as a fruitful methodology with examples ranging from 2D corpus callosum segmentation [...]

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 [...]

Fully automatic brain segmentation using model-guided level sets and skeleton-based models
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A fully automatic brain segmentation method is presented. First the skull is stripped using a model-based level set on T1-weighted inversion recovery images, then the brain ventricles and basal ganglia are segmented using the same method on T1-weighted [...]

Fuzzy Magnetic Color Image Segmentation  and  Advanced Edge Detection
No opinion
In this paper, color image segmentation based on fuzzy logic has been studied. Anefficient Fuzzy logic inference engine based on magnetic fields has been implemented in this project so as to intelligently extract color information in the given image and [...]

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 [...]

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 [...]

Auto-kNN: Brain Tissue Segmentation using Automatically Trained k-Nearest-Neighbor Classification
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In this paper we applied one of our regularly used processing pipelines for fully automated brain tissue segmentation. Brain tissue was segmented in cerebrospinal fluid (CSF), gray matter (GM) and white matter (WM). Our algorithms for skull stripping, tissue [...]

Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning
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In radiation treatment (RT) planning medical doctors need to consider a variety of information sources for anatomical and functional target volume delineation. The validation and inspection of the defined target volumes and the resulting RT plan is a complex [...]

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 [...]

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 [...]


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