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Improving The Oriented Image Class For Use In The Registration Framework
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The original design of the ITK registration framework was based around the itk::Image class, which assumed that the pixel axes were aligned with the coordinate system axes. The itk::OrientedImage was added later as a subclass, but problems remain with its [...]

Data, data everywhere, nor an image to read - Finding open image databases.
No opinion
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 [...]

Combining labeled images with ITK
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Combining some labeled images is a quite common and useful task in image analysis. That's something we may want to do to prepare the markers for a watershed from markers for example, or to write the output of several segmentations in a single file. This [...]

An image sampling framework for the ITK
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This document describes the implementation of image samplers using the Insight Toolkit ITK url{www.itk.org}. Image samplers take a set of `picks' from an image and store them in an array. A sample consists of the location of the pick (a point) and the [...]

Image Kernel Convolution
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Convolution is a basic operation in image analysis and the Insight Toolkit provides a well-framed mechanism for such operations (see Chapter 11 of the ITK Software Guide. The classes associated with this contribution are meant to simplify convolution [...]

An ITK implementation of the Normalized Gradient Field Image to Image Metric
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This article describes the ITK implementation of a Normalized Gradient Fields based image-to-image metric. Some properties of the metric are discussed and example registrations are presented.

Using and Visualizing Projective Cameras in VTK
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This document presents a set of classes (vtkPhysicalCamera, vtkImageCamera) to enable a camera and an image acquired by that camera to be visualized in a 3D scene. Two situations where one would want to visualize camaras with associated images are range data [...]

Entropy Image Filter
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This paper describes an intensity image filter for computing the entropy of pixel values contained within a neighborhood centered at each input pixel. The output image contains the calculated entropy for each input pixel location. This paper is accompanied [...]

Criminisi Inpainting
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This document presents a system to fill a hole in an image by copying patches from elsewhere in the image. These patches should be a good continuation of the hole boundary into the hole. The patch copying is done in an order which attempts to preserve linear [...]

Some extra image logical operations
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Logic operations such as $I > J$, where I and J are images are useful when generating masks. This submission includes $==$, $>$, $>=$, $<$ and $<=$ filters based on the existing logic filters. This is a very minor submission - there may already be easy [...]

Applying Image Mining to Support Gestational Age Determination
No opinion
The gestational age (GA) determination is one of the most used measures to guide diagnostics of specialists in neonatology to guarantee the newborn surveillance. However, the currently available methods have been subject to a number of evaluations and [...]

OpenITGLinkMUSiiC: A Standard Communications Protocol for Advanced Ultrasound Research
No opinion
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, [...]

Efficient contour detection in binary and label images
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ly in ITK, the only way to find the contour of the objects in a binary image is to use the BinaryErodeImageFilter, with a kernel of radius 1. This filter is a generic filter, made to support any shape and size of structuring element, and thus is not optimized [...]

Alternative Memory Models for ITK Images
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By default ITK images use a contiguous memory model. This means pixel elements are stored in a single 1-D array, where each element is adjacent in memory to the previous element. However in some situations it is not desirable to use this memory model. This [...]

The watershed transform in ITK - discussion and new developments
No opinion
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 [...]

The SIGN: A dynamic and extensible software framework for Image-Guided Therapy
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The software requirements for computer-aided navigation tools in image-guided therapy are becoming increasingly complex as a result of new possibilities in imaging and tracking hardware, novel application areas and regulatory restrictions. A new software [...]

Guided Diffusion Tensor Tractography with GTRACT: A Validation Study
No opinion
A novel fiber tracking algorithm (GTRACT) was developed to enhance tracking through ambiguous regions where cross fibers, fiber merging or fanning may be occurring. The software was developed using several cross platform open-source toolkits (ITK, VTK, and [...]

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. [...]

Advanced Normalization Tools: V1.0
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We provide examples and highlights of Advanced Normalization Tools (ANTS) that address practical problems in real data. A variety of image and point similarity metrics and elastic, diffeomorphic, affine and other variations of transformation models are [...]

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

An Image Filter for Counting Pixel Neighbors
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This papers describes an image filter that counts the number of neighbors a pixel has storing that value at the pixel's image index. Functionality is provided to 1) adjust the neighborhood size, 2) count only those pixels within a specific value range, and 3) [...]

Variance Image Filter
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This paper describes an intensity image filter for computing the variance of pixel values contained within a neighborhood centered at each input pixel. The output image contains the calculated variance at each input pixel location. Variance calculations can [...]

A Fast Approximation to the Bilateral Filter for ITK
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This document describes an implementation of an alternative bilateral filtering algorithm in ITK. This class implements the fast bilateral filter algorithm in ITK by taking the input image and organizing it into the required data structure as an ITK Image [...]

Simple directional gradients
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It is often useful to be able to compute the component of image gradient in a direction defined by a shape of some form, rather than relative to the image axis. This article introduces a simple method for doing this based on distance transforms that 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, [...]

RLEImage: run-length encoded memory compression scheme for an itk::Image
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This document describes a new class, itk::RLEImage, which uses run-length encoding to reduce the memory needed for storage of label maps. This class is accompanied by all the iterators to make it a dropin replacement for itk::Image. By changing the image [...]

Adaptations of MARACAS algorithm to the segmentation of the carotid bifurcation and stenosis quantification in CTA images
No opinion
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 [...]

Direct Fourier Tomographic Reconstruction Image-To-Image Filter
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We present an open-source ITK implementation of a direct Fourier method for tomographic reconstruction, applicable to parallel-beam x-ray images. Direct Fourier reconstruction makes use of the central-slice theorem to build a polar 2D Fourier space from the [...]

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, [...]

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 [...]

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 [...]

MORPHIAS: Molecular Phenotyping Image Analysis System
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Visualizing metabolic phenotypes, tracking phenotype dynamics, and screening molecular interventions all require comprehensive, quantitative measures of micromolecular patterns across cell classes. In this project we develop an easy-to-use interface that [...]

The NLM-Mayo Image Collection: Common Access to Uncommon Data
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For over two decades, the National Library of Medicine (NLM) has provided support for the collection of biomedical image data for use throughout the biomedical image, visualization and analysis community. Data collected during the Visible Human Project has [...]

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 [...]

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 [...]

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 [...]

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 [...]

Generalizing vesselness with respect to dimensionality and shape
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In this paper we present a generalization of Frangi's vesselness measure cite{Frangi1998} for the enhacement of M-dimensional shapes in N-dimensional images, together with the implementation of the corresponding Insight Toolkit (ITK) filter [...]

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 [...]

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

IGSTK: Building High Quality Roads with Open Source Software
No opinion
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 [...]

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 [...]

Image Registration with Automatic Computation of Gradients
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Many image registration algorithms are formulated as optimization problems with a gradient descent based solver, One difficulty with designing and implementing such methods is in the implementation of 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 [...]

CustusX: A Research Application for Image-Guided Therapy
No opinion
CustusX version 3 is an in-house application for research in image-guided therapy with a focus on intraoperative use and ultrasound imaging. It is built upon open source toolkits such as the Insight Toolkit (ITK), the Visualization Toolkit (VTK), Qt and [...]

Skull Base Surgery Navigation System Based on Updating Preoperative Images Using Positional Information of Surgical Tools
No opinion
In this paper, we introduce a new concept of surgical navigation which processes information interactively between the real and virtual spaces, namely, updating preoperative images using the positional information of surgical tools. Although the organs are [...]

OpenIGTLink Protocol Version 2
No opinion
In this paper, we review the technical details of new features in OpenIGTLink version 2. OpenIGTLink is a free open-source network communication protocol designed for data exchange among devices and software. Since the first release of version 1.0 protocol [...]

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 [...]

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 [...]

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 [...]

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 [...]

Automatic Conductance Estimation Methods for Anisotropic Diffusion ITK Filters
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The anisotropic diffusion algorithm has been intensively studied in the past decades, which could be considered as a very efficient image denoising procedure in many biomedical applications. Several authors contributed many clever solutions for diffusion [...]

The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations
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This paper describes the Datatree module of BioImage Suite, that allows for rapid and flexible reslicing of images based on a user-defined tree structure that organizes image and transformation data as well as electrode localizations, image landmarks, and [...]

Image Calculator
No opinion
ImageCalculator is a command line program for doing simple mathematical operations to a series of images and generating an new output image and basic statistics about the output image. The program uses the Insight Toolkit (www.ITK.org) for file IO and [...]

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 [...]

Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK
No opinion
The Allen Brain Atlas (ABA) project aims to create a cellular-resolution, genome-wide map of gene expression in the adult mouse brain. The resulting in situ hybridization (ISH) image data will be available free-of-charge to the public. Additionally, we [...]

Scale Invariant Feature Transform for n-Dimensional Images (n-SIFT)
No opinion
This document describes the implementation of several features previously developed[2], extending the 2D scale invariant feature transform (SIFT)[4, 5] for images of arbitrary dimensionality, such as 3D medical image volumes and time series, using ITK1. [...]

Using a Mask to Decrease Computation Time for SpatialObject to Image Conversions
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This article presents an approach for decreasing the computational time for converting a sparse SpatialObject to an Image. The method is applicable for SpatialObjects which occupy less volume than the total output Image (which occurs often, especially when [...]

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

Realistic And Efficient Brain-Skull Interaction Model For Brain Shift Computation
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In this paper we propose the usage of a very efficient contact implementation for modeling the brain-skull interaction. This contact algorithm is specially design for our Dynamic Relaxation solution method for solving soft-tissue registration problems. It [...]

A Voodoo Reader and Viewer for VTK
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Voodoo is a popular, free structure from motion software package. It takes several, ordered images as input and computes the camera parameters of each image as well as a point cloud of an estimate of the 3D structure of the scene. This document presents a set [...]

Carotid arteries segmentation in CT images with use of a right generalized cylinder model
No opinion
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 [...]

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

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 [...]

A software architecture for cell manipulation
No opinion
A software architecture has been developed for image-guided robot-assisted cell manipulation. The system provides tools for positioning and navigation of multiple micromanipulators under live microscope images. The main application of this system is in [...]

A Lightweight and Portable Communication Framework for Multimodal Image-Guided Therapy
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In today’s medicine a lot of research revolves around the combination of different imaging and tracking modalities to form a new system for Image-Guided Therapy. Such systems can help to overcome shortcomings of the individual techniques or create new kinds [...]

MUSiiC ToolKit 2.0: Bidirectional Real-time Software Framework for Advanced Interventional Ultrasound Research
No opinion
Ultrasound (US) imaging is a popular and convenient medical imaging modality thanks to its mobility, non-ionizing radiation, ease-of-use, and real-time acquisition. Conventional US imaging is frequently integrated with tracking systems and robotic systems in [...]

2D/3D Multi-Modality Image Registration in Non-Destructive Evaluation
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Non-destructive evaluation(NDE) is a group of analysis techniques used in industry to evaluate the property of a material, component or product without causing damage. Among all the techniques, radiology and thermography are two most common methods that are [...]

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 [...]

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 [...]

ITK Image IO interface with Apple iOS
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We have recently detailed the procedure for building ITK on the iOS. In this work, we contribute itkiOSImageIO , the necessary ITK class that provides the input/output (IO) interface with the repository of images stored on iOS Apple devices, such as the iPod [...]

Itk::Transforms supporting spatial derivatives
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This document describes the use and implementation of first and second order spatial derivatives of coordinate transformations in the Insight Toolkit url{www.itk.org}). Spatial derivatives are useful for many types of regularising or penalty terms frequently [...]

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 OpenCL implementation of the Gaussian pyramid and the resampler
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Nonrigid image registration is an important, but resource demanding and time-consuming task in medical image analysis. This limits its application in time-critical clinical routines. In this report we explore acceleration of two time-consuming parts of a [...]

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 [...]

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 [...]

A programming environment for the development of modular 3D biomedical image processing applications
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ImageLib is a free object-oriented development environment destined to biomedical image processing. The software package contains a programming library (C++ language) and an MDI user interface (kernel). The major interest is to allow the creation of fully [...]

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, [...]

An Architecture Validation Toolset for Ensuring Patient Safety in an Open Source Software Toolkit for Image-Guided Surgery Applications
No opinion
As open source software projects gain acceptance in mission critical domains of a technology-enabled society, they must adapt their lightweight processes and tools to address the quality needs of these domains. One such domain is technology-supported [...]

Tetrahedral mesh generation for medical imaging
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We describe the open source implementation of an adaptive tetrahedral mesh generator particularly targeted for non-rigid FEM registration of MR images. While many medical imaging applications require robust mesh generation, there are few codes available. [...]

IGSTK: A State Machine Architecture for an Open Source Software Toolkit for Image-Guided Surgery Applications
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The Image-Guided Surgery Toolkit (IGSTK) is an Open Source software project being developed under NIH/NIBIB funding. The toolkit will provide a common platform for implementing image-guided surgery applications and for fostering research in the field. The [...]

3D Voxel-Based Volumetric Image Registration with Volume-View Guidance
No opinion
In this article, we will present a novel interactive image registration technique using the 3D volumetric view as guidance throughout the registration process. The registration criterion used in this technique is the homogeneity of the color distribution on [...]

An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open-source software
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This paper describes a new open-source tutorial for image-guided therapy (IGT) and medical robotics that is both accessible and hands-on using the LEGO Mindstorms NXT (a commercially available robotics kit) and 3D Slicer (an open-source application for [...]

FusionViewer: An Open Source Toolkit for Viewing Multimodality Images
No opinion
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) [...]

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 [...]

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

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

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 [...]

Unified framework for development, deployment and testing of image analysis algorithms
No opinion
Developing both graphical and command-line user interfaces for image analysis algorithms requires considerable effort. Generally developers provide limited to very rudimentary user interface controls to their users. These image analysis algorithms can only [...]

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 [...]

Biomarker Detection in Whole Slide Imaging based on Statistical Color Models
No opinion
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 [...]

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 [...]

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 [...]

Voxelizer plug-in for Blender
No opinion
This document describes a plug-in for Blender (www.blender.org) that allows to rasterize 3D mesh objects into 3D voxel data, i. e. it allows to voxelize Blender meshes. In 2D, this process can be compared to rasterization of vector graphics into pixel [...]

A 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. [...]

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 [...]

Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation
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Modern medical imaging analyses often involve the concatenation of multiple steps, and neuroimaging analysis is no exception. The Java Image Science Toolkit (JIST) has provided a framework for both end users and engineers to synthesize processing modules into [...]

I-DO: A Deformable Organisms framework for ITK
No opinion
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 [...]

Transitively Consistent and Unbiased Multi-Image Registration using Numerically Stable Transformation Synchronisation
No opinion
Transitive consistency of pairwise transformations is a desirable property of groupwise image registration procedures. The transformation synchronisation method (Bernard et al., 2015) is able to retrieve transitively consistent pairwise transformations from [...]

An ITK-Based Framework for 2D-3D Registration with Multiple Fixed Images
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This document describes an extension of the Insight Toolkit (ITK, www.itk.org) for 2D-3D registration with multiple fixed images, that is, registration of a three-dimensional dataset to a group of fixed planar projections. 2D-3D registration is possible with [...]

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 [...]

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 [...]

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 [...]

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 [...]

Automatic Segmentation of Head and Neck CT Images by GPU-Accelerated Multi-atlas Fusion
No opinion
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
No opinion
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 [...]

Flux driven medial curve extraction
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In this document it is described the implementation of the flux driven automatic centerline extraction algorithm proposed by Bouix et al. in 2004. This is based on a skeletonisation algorithm initially proposed by Siddiqi et al. in 2002, using properties of [...]

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 [...]


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