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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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

Liver Tumor segmentation in CT images using probabilistic
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Liver tumors segmentation is an important prerequisite for planning of surgical interventions. For clinical applicability, the segmentation approach must be able to cope with the high variation in shape and gray-value appearance of the liver. We present a [...]

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. [...]

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 [...]

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 [...]

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, [...]

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 [...]

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 [...]

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. [...]

Data, data everywhere, nor an image to read - Finding open image databases.
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Open Science includes access to both open source software/methodologies and open data. While there has been progress in open image databases, the results of these efforts are under-reported. As such, imaging scientists are unaware of the available data. In [...]

Fuzzy Magnetic Color Image Segmentation  and  Advanced Edge Detection
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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 [...]

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

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 [...]

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 [...]

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 [...]

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 [...]

Go-Go Gabor Gadgetry
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Although Gabor filtering is quite prevalent in the computer vision community for such tasks as texture segmentation and motion analysis, such capabilities are conspicuously absent from the Insight Toolkit. The contribution described in this paper attempts [...]

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, [...]

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 [...]

Adapting the ITK Registration Framework to Fit Parametric Image Models
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The image registration framework in the Insight Tookit offers a powerful body of code for finding the optimal spatial transform that registers one image with another. However, ITK currently lacks a way to fit parametric models of image pixel values to an [...]

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 [...]

Real-Time Ultrasound Image Analysis for the Insight Toolkit
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We have successfully created a software environment in which ultrasound data can be manipulated by, ITK (the Insight Tool-Kit), in real-time. We were able to access each frame generated within the resident computer of a TerasonTM Ultrasound Machine, convert [...]

An open, clinically-validated database of 3D+t cine-MR images of the left ventricle with associated manual and automated segmentation
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In this paper, we describe a database of cine-MR (3D+t) images of the left ventricle. This database contains the voxel data, one automated and two manual segmentations for each sequence of images. The segmentations are validated from a clinical point of [...]

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 [...]

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 [...]

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 [...]

Cumulative Gaussian Curve Fitter for Boundary Parameterization
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We have previously developed an algorithm for locating boundaries in an image with sub-pixel resolution, as well as estimating boundary width and image intensity within the adjoining objects. The algorithm operates by finding the parameters of a cumulative [...]

Minimally Interactive Knowledge-based Coronary Tracking in CTA using a Minimal Cost Path
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An algorithm for minimally interactive coronary artery tracking is presented. Tracking ability and accuracy results are demonstrated on 16 images CTA images. First, a region of interest is automatically selected and a denoising filter applied. Then, for each [...]

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 [...]

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 [...]

The Lung Tissue Research Consortium:  An extensive open database containing histological, clinical, and radiological data to study chronic lung disease
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The Lung Tissue Research Consortium (LTRC) is an NHLBI sponsored project which is studying histological, radiological, and clinical data on patients with Chronic Obstructive Pulmonary Disease (COPD) and idiopathic pulmonary fibrosis (IPF). At completion, [...]

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) [...]

A Label Geometry Image Filter for Multiple Object Measurement
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The itkLabelGeometryImageFilter is a new ITK filter that enables the measurement of geometric features of labeled objects. It calculates features similar to the "regionprops" command of Matlab. It is related to the itkLabelStatisticsImageFilter in that both [...]

An open-source real-time ultrasound reconstruction system for four-dimensional imaging of moving organs
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Four-dimensional imaging is a necessary step in computer-assisted interventions (CAI) performed on moving surgical targets, such as those located within the beating heart or influenced by respiratory motion. Ultrasound (US) is often the best imaging modality [...]


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