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Automated Walks using Machine Learning for Segmentation
No opinion
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 [...]

Perspectives on Image-Guided Transapical Beating Heart Aortic Valve Intervention
No opinion
Image-guided interventional systems become an essential part of the modern minimally invasive surgical procedures, especially for the cardiac surgery. Transapical aortic valve implantation (TAVI) is a recently developed surgical technique to treat severe [...]

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 [...]

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 [...]

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 [...]

Gaussian Intensity Model with Neighborhood Cues for Fluid-Tissue Categorization of Multi-Sequence MR Brain Images
No opinion
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 [...]

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

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

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 [...]

Automatic Mandible Segmentation on CT Images Using Prior Anatomical Knowledge
No opinion
We present a fully automatic method for segmenting mandible in CT images using anatomic landmarks and prior knowledge. The aim is to utilize spatial relationship of anatomic landmarks with image processing techniques to detect mandible robustly and [...]

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 [...]

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 [...]

An implementation of the minimization of region-scalable fitting energy levelsets
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Intensity inhomogeneities often occur in medical images, especially when using magnetic resonance imaging. In these images, the standard Chan-and-Vese levelset segmentation method may not work properly, as it assumes constant intensity distributions for [...]

Gauss-Newton Method for Segmentation assisted Deformable Registration
No opinion
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 [...]

Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning
No opinion
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 [...]

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 [...]

Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates
No opinion
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 [...]

Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut
No opinion
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 [...]

Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge
No opinion
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 [...]

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 [...]

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 [...]

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 [...]

A Skull-Stripping Filter for ITK
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Skull-stripping (or brain extraction) is an important pre-processing step in neuroimage analysis. This document describes a skull-stripping filter implemented using the Insight Toolkit ITK, which we named itk::StripTsImageFilter. It is a composite filter [...]

Inverting deformation fields using a fixed point iteration scheme
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Being able to quickly compute the inverse of a deformation field is often useful in the context of medical image analysis. While ITK supports this functionality, the current algorithms are slow and do not always yield accurate results. In this paper we [...]

A Multi-atlas Approach for the Automatic Segmentation of Multiple Structures in Head and Neck CT Images
No opinion
A multi-atlas approach is proposed for the automatic segmentation of nine different structures in a set of head and neck CT images for radiotherapy. The approach takes advantage of a training dataset of 25 images to build average head and neck atlases of [...]

Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching
No opinion
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 [...]

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 [...]

Fully Automatic Segmentation of Head and Neck Organs using Active Appearance Models
No opinion
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 [...]

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, [...]

Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models
No opinion
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
No opinion
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 [...]

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 [...]

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 [...]

Pseudo-CT generation from multiple MR images for small animal irradiation
No opinion
Introduction. Computed tomography (CT) is the standard imaging modality for radiation therapy treatment planning (RTTP) because of its ability to provide information on electron density. However, magnetic resonance (MR) imaging provides superior soft tissue [...]

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. [...]

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 [...]

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 [...]

On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands
No opinion
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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

Shaped Neighborhood based Flood Filled Conditional Iterators
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ITK's flood filling iterator represents a way to visit pixels/voxels within an image having a specific connectivity. The iterator is initialized at known seed points and starting from these, neighbors that are within the desired connectivity are marked as to [...]

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 [...]

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

MAP–Based Framework for Segmentation of MR Brain Images Based on Visual Appearance and Prior Shape
No opinion
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 [...]

The Image-based Vascular Analysis Toolkit (IvanTk)
No opinion
This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an [...]

Auto-kNN: Brain Tissue Segmentation using Automatically Trained k-Nearest-Neighbor Classification
No opinion
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 [...]

Multimodal Analysis of Vasogenic Edema in Glioblastoma Patients for Radiotherapy Planning
No opinion
Glioblastoma (GBM) is the most common type of primary brain tumor, which is characterized by an infiltrative growth pattern. In current practice, radiotherapy planning is primarily based upon T2 FLAIR MRI despite its known lack of specificity in the detection [...]

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 [...]

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 [...]

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 [...]

Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS)
No opinion
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 [...]

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 [...]

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 [...]

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 [...]

Minimally Interactive Knowledge-based Coronary Tracking in CTA using a Minimal Cost Path
No opinion
An algorithm for minimally interactive coronary artery tracking is presented. Tracking ability and accuracy results are demonstrated on 16 images CTA images. First, a region of interest is automatically selected and a denoising filter applied. Then, for each [...]

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


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