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Tagged Volume Rendering of the Heart: A Case Study
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This is a companion paper describing the process and parameters for tagged volume rendering of the heart. We firstly review the relevant concepts and consider the problem of visualising the coronary arteries from computed tomography angiography (CTA) images. [...]

SharpImage: An Image Processing Prototyping Environment
No opinion
This paper describes an image processing prototyping environment called SharpImage. SharpImage is a stand-alone Windows application geared towards the pre-processing and creation of volume illustrations, although other generic tasks are inherently supported. [...]

Using a Mask to Decrease Computation Time for SpatialObject to Image Conversions
No opinion
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 [...]

ManagedITK: .NET Wrappers for ITK
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ManagedITK generates wrappers around ITK for .NET languages. These wrappers can be used with any CLR language, including C#, VB.NET, IronPython, and others. ManagedITK is useful for a number of reasons, including the ability to rapidly create graphical user [...]

ImageNetworkReader: an ITK Class for Loading Images Across a Network
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This document describes a new class for the Insight Toolkit~(ITK www.itk.org) for reading images across a network. Network access is handled by CURL (http://curl.haxx.se/libcurl/), an Open Source library for client-side URL transfer. CURL supports the FTP, [...]

An alternative threading model for the Insight Toolkit
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This technical note presents an alternative threading model for the Insight Toolkit. The existing ITK threading model is based on a "scatter / gather" model and divides work evenly amongst all threads. Though suitable for many filters, considerations such [...]

RANSAC Plane Fitting for VTK
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RANdom SAmple Concensus (RANSAC) is an iterative method to estimate parameters of a model. It assumes that their are inliers in the data which are well explained by the chosen model. We propose a new class for VTK, vtkRANSACPlane, which estimates the best [...]

A Leica PTX Reader for VTK
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Leica LiDAR scanners output points in the PTX file format. It is often useful to convert this format to a standard VTK point cloud or mesh format before processing. We propose a new class, vtkPTXReader, to provide this functionality.

Stratified Mesh Sampling for VTK
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This document presents an implementation of a stratified mesh sampling algorithm in the VTK framework. This code was adapted directly from the original implementation by Diego Nehab, with permission. We present a class, vtkStratifiedSampling, which uniformly [...]

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 [...]

A Mesh Front Iterator for VTK
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Region growing is a technique that can be used to propagate information over a mesh. We provide an iterator that can be used with vtkPointSet subclasses to traverse a mesh in a reasonable fashion. A "front" is emanated from a selected starting vertex, and the [...]

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 [...]

A Conditional Mesh Front Iterator for VTK
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Region growing is a technique that can be used to propagate information over a mesh. In a previous submission, "A Mesh Front Iterator for VTK", we introduced an iterator that can be used with vtkPointSet subclasses to traverse a mesh. It is sometimes useful [...]

A Synthetic LiDAR Scanner for VTK
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In recent years, Light Detection and Ranging (LiDAR) scanners have become more prevalent in the scientific community. They capture a "2.5-D" image of a scene by sending out thousands of laser pulses and using time-of-flight calculations to determine the [...]

Expectation Maximization of Gausian Mixture Models in VTK
No opinion
Expectation maximization (EM) is a common technique for estimating the parameters of a model after having collected observations of data generated by the model. We first explain the algorithm, then present our impelementation. We focus on estimation of the [...]

A VTK Interface for the Hokuyo UTM 30LX Laser Range Finder
No opinion
It is convenient to acquire data in a format which VTK can read directly. To enable this, we provide a wrapper of the Hokuyo UTM-30LX interface in a class vtkHokuyo. The code is currently hosted at git@github.com:daviddoria/vtkHokuyo.git. This class only [...]

A Mean Shift Clustering Implementation for VTK
No opinion
Mean shift clustering is an excellent technique for clustering points when the number of clusters is not known. We present a implementation (vtkMeanShiftClustering) of the simplest version of the algorithm written in a VTK context. The code is currently [...]

Using the strategy pattern to simplify ITK
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ITK is becoming increasingly complex as it continues to grow and evolve. The SimpleITK initiative aims to address this concern by providing an easy-access layer around ITK for non-C++ expert developers. This article proposes an alternate (perhaps [...]

Point Set Surface Reconstruction for VTK
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This document presents a set of classes (vtkPointSetSurfaceReconstruction, vtkVoxelizePolyData) to produce a surface from an oriented point set. These classes are implemented as VTK filters. A Paraview plugin interface is provided to allow extremely easy [...]

Poisson Editing in ITK
No opinion
This code provides an implementation of two techniques from ``Poisson Image Editing'' on ITK images. First, we fill a hole in an image given only the pixel values on the boundary. Second, we copy a patch of an image into another image and make the result as [...]

Loopy Belief Propagation on MRFs in ITK
No opinion
This code provides a base implementation of Loopy Belief Propagation on MRFs in ITK. We use binary image denoising as an example problem to demonstrate this code. This document is intended only to describe the implementation, not the theory. A complete [...]

Criminisi Inpainting
No opinion
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 [...]

Morphological Opening on a Graph
No opinion
This document presents an implementation of an algorithm to perform a morphological opening on a graph. The intent is to remove short branches in a graph while preserving the large scale structure. This implementation is based on the algorithm described in [...]

Closed Loop Simplification
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This document presents an implementation of an algorithm to find a low edge-count approximation of a complex, discrete, 2D closed contour. This implementation is based on the algorithm described in ``Using Aerial Lidar Data to Segment And Model Buildings'' [...]

Point Set Processing for VTK - Outlier Removal, Curvature Estimation, Normal Estimation, Normal Orientation
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This document presents a set of classes (vtkPointSetOutlierRemoval, vtkPointSetNormalEstimation, vtkPointSetNormalOrientation, vtkPointSetCurvatureEstimation, vtkEuclideanMinimumSpanningTree, and vtkRiemannianGraphFilter) to enable several basic operations on [...]

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 [...]

Moore Neighbor Tracing
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This document presents an implementation of Moore Neighbor Tracing - an algorithm to find an ordered outline of a blob or contour in an image. An excellent tutorial on Moore Neighbor Tracing is provided [...]

Small Hole Filling in ITK
No opinion
This code provides an implementation of a simple technique to fill small holes in an image. We use a multi-pass method that fills pixels on the border of a hole with the average of its non-hole 8-connected neighbors. This process is repeated until all holes [...]

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 [...]

ItkImageFunctionImageFilter: A New Filter To Apply An itkImageFunction To Every Pixel In An itkImage
No opinion
This document presents a new class to apply an itkImageFunction to every pixel in an itkImage. This functionality is almost identical to itkUnaryFunctorImageFilter, but it uses an itkImageFunction rather than an itk::Functor. As some functionalities in ITK [...]

A Wavefront OBJ Writer for VTK
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The Wavefront OBJ format is a common file format for storing mesh data. It is convenient to be able to write VTK data structures out into this format, as the data can then be used in software that can read OBJ files.

Interactive Correspondence Selection
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This document presents a GUI application to manually select corresponding points in two data sets. The data sets can each be either an image or a point cloud. If both data sets are images, the functionality is equivalent to Matlab's 'cpselect' function. There [...]

A K-Means++ Clustering Implementation for VTK
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K-Means clustering is an excellent technique for clustering points when the number of clusters is known. We present a implementation (vtkKMeanClustering) of the algorithm written in a VTK context. We also implement the K-Means++ initialization method which [...]

A small rework for the Gaussian Derivative Image Function
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The itk::GaussianDerivativeImageFunction computes the derivative at the specified physical or pixel location. Unfortunately it has a number of deficiencies, for which I suggest possible solutions.

ComposeRGBA
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This article presents the itk::ComposeRGBAImageFilter.

Transforming an itkPointSet
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This document presents a set of classes to enable operations on itkPointSet objects. In particular, itkTransformPointSetFilter allows a transformation to be applied to a set of points. We propose these classes as addition to the Insight Toolkit ITK.

Region Growing Using a Criterion on the Region Boundary
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This document presents a set of classes which implement a region growing algorithm whose criterion for growth is different than existing ITK region growing algorithms. The region is grown into the query pixel based only on the difference between the query [...]

LookAt Transform Initializer and Oblique Section Image Filter
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This paper describes the ITK implementation of a transform initializer to produce a rigid 3-D transform able to center a given point on an arbitrary plane. The resultant transform allows the user to "look at" a point from a given direction. The resultant [...]

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 [...]

Reading a PTX file into an itkMesh
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This document presents a set of classes to read a PTX file (a common file format produced by LiDAR scanners) into an itkMesh object. We propose these classes as addition to the Insight Toolkit ITK (www.itk.org).

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 [...]

Cuberille Implicit Surface Polygonization for ITK
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This article describes an ITK implementation of the "cuberille" method for poloygonization of implicit surfaces. The method operates by dividing the surface into a number of small cubes called cuberilles. Each cuberille is centered at a pixel lying on the [...]

Perturbing Mesh Vertices with Additive Gaussian Noise
No opinion
This brief document provides an introduction to an external ITK module, DVMeshNoise. This module provides classes for perturbing the positions of the vertices of either an itk::Mesh or itk::QuadEdgeMesh with Gaussian noise. This may be useful in testing the [...]

Hough Transform Plane Detector
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This document presents a VTK wrapper of an extracted portion of ‘3DTK - The 3D Toolkit’ (http://threedtk.de) to enable a developer to find planes in 3D point cloud data.

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 [...]

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

Simultaneous Manifold Learning and Clustering: Grouping White Matter Fiber Tracts Using a Volumetric White Matter Atlas
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We propose a new clustering algorithm. This algorithm performs clustering and manifold learning simultaneously by using a graph-theoretical approach to manifold learning. We apply this algorithm in order to cluster white matter fiber tracts obtained [...]

A Framework for Improved Regression Testing Based Upon CTest and CDash
No opinion
The existing CMake and CTest environment provides an excellent platform for execution and submission of software quality tests. However, there is little support or aid for regression type tests provided to lessen the burden of writing tests and verifying 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 [...]

Smart Nearest Neighbors
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This document presents an implementation of two algorithms, Voronoi Neighbors and Binary Space Partition (BSP) Neighbors. These algorithms find neighbors of a point in a point set that are somehow ``better'' than a ``K nearest neighbors'' or a ``all neighbors [...]

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 [...]

Efficient N-Dimensional surface estimation using Crofton formula and run-length encoding
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Unlike the measure of the area in 2D or of the volume in 3D, the perimeter and the surface are not easily measurable in a discretized image. In this article we describe a method based on the Crofton formula to measure those two parameters in a discritized [...]

BinShrink: A multi-resolution filter with cache efficient averaging.
No opinion
We present a new filter for the Insight Toolkit (ITK) for reducing the resolution of an image by an integer factor while averaging called BinShrink. This filter provides a new level of performance to ITK for reducing resolution and noise present in an image. [...]

A Streaming IO Base Class and Support for Streaming the MRC and VTK File Format
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This paper describes our contribution of three new classes to the Insight Toolkit community. We present a new ImageIO base class for streaming image file, along with two derived ImageIO classes for the VTK and the MRC file formats.

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 [...]

Poisson Surface Reconstruction for VTK
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This document presents an implementation of the Poisson surface reconstruction algorithm in the VTK framework. (This code was, with permission, adapted directly from the original implementation by Kazhdan, Bolitho, and Hugues. The original implementation can [...]

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 [...]

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 [...]

N-Dimensional Phase Unwrapping
No opinion
Although phase data can take on any value, it is generally only possible to measure phase as a principle value, i.e., wrapped within the range (-pi,pi]. Determining the unwrapped phase from its principle value is a topic of considerable interest in magnetic [...]

The Generalised Image Fusion Toolkit (GIFT)
No opinion
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, [...]

A DICOM-based Software Infrastructure for Data Archiving
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In this paper , we propose an extension to the National Library of Medicine's Insight Segmentation and Registration Toolkit (ITK. www.itk.org) with a companion image access and archival system that merges the image transfer capabilities of DICOM with DSpace [...]

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 [...]

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 [...]

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 [...]

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

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 [...]

Multilocal Creaseness Measure
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This document describes the implementation using the Insight Toolkit of an algorithm for detecting creases (ridges and valleys) in N-dimensional images, based on the Local Structure Tensor of the image. In addition to the filter used to calculate the [...]

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 [...]

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 [...]

Adding Refined Isosurface Rendering and Shadow Mapping to vtkGPUVolumeRayCastMapper
No opinion
In the medical simulation world the use of isosurfaces is a common action, as the information from some sources, e.g. CTs, is very well defined, and the isosurface can be easily set. Additionally, in any simulator shadows are a necessary addition to increase [...]

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 [...]

A Modification to Otsu Thresholding Method for ICV Segmentation
No opinion
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.

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 [...]

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 [...]

Spherical Wavelet ITK Filter
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This paper describes the Insight Toolkit (ITK) Spherical Wavelet object: itkSWaveletSource. This ITK object is an implementation of a paper by Schr¨oder and W. Sweldens, “Spherical Wavelets: Effi- ciently Representing Functions on the Sphere” [8], with [...]

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

Contrast Enhancement for Liver Tumor Identification
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In CT images, tumors located in a liver are generally identified by intensity difference between tumor and liver. The intensity of the tumor can be lower and or higher than that of the liver. However, the main problem of liver tumor detection from is related [...]

Multiple Sclerosis Detection in Multispectral Magnetic Resonance Images with Principal Components Analysis.
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This paper presents a local feature vector based method for automated Multiple Sclerosis (MS) lesion segmentation of multi spectral MRI data. Twenty datasets from MS patients with FLAIR, T1,T2, MD and FA data with expert annotations are available as training [...]

Head and Neck Auto-segmentation Challenge
No opinion
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 [...]

Multi-object Segmentation of Head Bones
No opinion
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 [...]

A framework for data and context integration in the modular digital OR
No opinion
Today, OR planning is supported by different clinical information systems. However, relevant patient information is distributed and spread over separate heterogeneous information systems (HIS, RIS, PACS), where each requires its own login and user interaction [...]

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 [...]

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 [...]

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 [...]

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

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

Non-negative matrix factorization framework for dimensionality reduction and unsupervised clustering
No opinion
Non-negative Matrix Factorization (NMF) is a robust approach to learning spatially localized parts-based subspace patterns in applications such as document analysis, image interpretation, and gene expression analysis. NMF-based decomposition capabilities are [...]

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 [...]

The Surgical Assistant Workstation
No opinion
The Surgical Assistant Workstation (SAW) is a software development framework that can be used to develop new applications in robot-assisted surgery with augmented visualization. Robot-assisted laparoscopic surgery and micro-surgery as presented by the da [...]

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 [...]

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, [...]

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 [...]

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

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 [...]

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 [...]

Construction of Statistical Shape Models from Minimal Deformations
No opinion
Abstract. Statistical shape models (SSM) capture the variation of shape across a population, in order to allow further analysis. Previous work demonstrates that deformation fields contain global transformation components, even if global pre- registration is [...]

A VTK-based, CUDA-optimized Non-Parametric Vessel Detection Method
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We present a VTK-based implementation of our non-parametric vessel detection method that identifies vascular structures using a polar neighborhood profile. To accelerate the computationally intensive parts of the algorithm, we leverage the hardware [...]

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 [...]

An Integrated Computer-Aided Robotic System for Dental Implantation
No opinion
This paper describes an integrated system for dental implantation including both preoperative planning utilizing computer-aided technology and automatic robot operation during the intra-operative stage. A novel two-step registration procedure was applied for [...]

LV Challenge LKEB Contribution: Fully Automated Myocardial Contour Detection
No opinion
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 [...]

An Open-Source Solution for Interactive Acquisition, Processing and Transfer of Interventional Ultrasound Images
No opinion
Ultrasound has become a very important modality in image-guided therapy. At present, however, the collection, synchronization and transfer of ultrasonic images are more cumbersome than necessary. This paper presents a reusable solution to these problems. We [...]

Validation of real-time intensity based 2D/3D registration for image guided radiotherapy
No opinion
Patient motion during radiotherapy or intra-fractional motion, is one of the major sources of uncertainty in dose application. 2D/3D registration is an intensity based method used successfully to track tumor motion with the potential to reduce uncertainty. [...]

Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images
No opinion
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
No opinion
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 [...]

Local Shape Analysis using MANCOVA
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Gross shape measures such as volume have been widely used in statistical analysis of anatomical structures. Statistical shape analysis methods have emerged within the last decade to allow for a localized analysis of shape. Most shape analysis frameworks are [...]

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 [...]

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 [...]

ReachIN: A Modular Vision Based Interface for Teleoperation
No opinion
Teleoperation is currently the dominant form of instrument control for surgical robotics. For example, the mechanical masters in the da Vinci surgical system provides a stable, precise interface for teleoperation, allowing execution of delicate tasks in [...]

Incorporating Metric Flows and Sparse Jacobian Transformations in ITK
No opinion
Various metrics have been proposed in the literature for performing intrinsic automatic image to image registration. Among these measures, mutual information is a very popular one because of its robustness and accuracy for a wide variety of applications. In [...]

Camino: Diffusion MRI reconstruction and processing
No opinion
Camino is an open-source, object-oriented software package for processing diffusion MRI data. Camino implements a data processing pipeline, which allows for easy scripting and flexible integration with other software. This paper summarises the features of [...]

Collaborative Development of an open framework for medical simulation
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This paper investigates an Open Framework for Medical Simulation (named SOFA for Simulation Open Framework Architecture), and proposes ideas for structuring and supporting its expansion. Lately, through a joint effort between the Sim Group at CIMIT and the [...]

3D Voxel-Based Volumetric Image Registration with Volume-View Guidance
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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 [...]

Software Architecture of a System for Robotic Surgery
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At the German Heart Center Munich we have installed and evaluated a novel system for robotic surgery. Its main features are the incorporation of haptics (by means of strain gauge sensors at the instruments) and partial automation of surgical tasks. [...]

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, [...]

Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM
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Shape analysis has become of increasing interest to the neuroimaging community due to its potential to precisely locate morphological changes between healthy and pathological structures. This manuscript presents a comprehensive set of tools for the [...]

Simulink Libraries for Visual Programming of VTK and ITK
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We have created open-source Simulink block libraries for ITK and VTK that allow pipelines for these toolkits to be built in a visual, drag-and-drop style within MATLAB. Each block contains an instance of an ITK or VTK class. Any block connections and [...]

Framework of US-guided therapeutic HIFU system for renal diseases
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The authors describe a framework for the US-guided therapeutic HIFU system for renal diseases. In particular, the HIFU system is integrated with robotic servoing capability so as to track quasi-periodically moving renal tumors and stones. The system is [...]

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

Robot assisted prostate surgery using augmented reality with deformable models
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We present preliminary results of our work to develop an augmented display for improved visualization of the prostate and surrounding critical anatomy for robot-assisted prostate surgery. Prostate cancer is the second leading cause of cancer-related deaths in [...]

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 [...]

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

Improvements in SlicerRT, the radiation therapy research toolkit for 3D Slicer
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Purpose: Recent years have seen growing interest in adaptive radiation therapy (RT), but the existing software tools are not ideal for research use, as they are either expensive and closed proprietary applications or free open-source packages with limited [...]

MR Parameter Map Suite: ITK Classes for Calculating Magnetic Resonance T2 and T1 Parameter Maps
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This document describes a suite of new multi-threaded classes for calculating magnetic resonance (MR) T2 and T1 parameter maps implemented using the Insight Toolkit ITK (www.itk.org). Similar to MR diffusion tensor imaging (DTI), MR T2 and T1 parameter maps [...]

InsightToolkit Kinetic Analysis (itk::ka) Library
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This paper describes how to compile and use the Insight Toolkit Kinetic Analysis library (itk::ka), to perform analysis of dynamic medical images, along with a brief overview of the library source code. Supplied, are a set of interfaces to facilitate [...]

IGSTK: Development Process and Project Management Best Practices for an Open Source Software Toolkit for Image-Guided Surgery Applications
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Open source technologies are increasing in popularity for software development. Many open source projects rely on skilled development teams whose members are distributed throughout the world. Often, agile development methods are employed by these teams, as [...]

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 [...]

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. [...]


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