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Label object representation and manipulation with ITK
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Richard Beare has recently introduced a new filter to efficiently labelize the connected components with ITK, and has also proposed to use the run-length encoding used in that filter to implement some of the most useful binary mathematical morphology [...]

Skull Base Surgery Navigation System Based on Updating Preoperative Images Using Positional Information of Surgical Tools
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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 [...]

Primal/Dual Mesh with Application to Triangular/Simplex Mesh and Delaunay/Voronoi
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This document describes an extension of ITK to handle both primal and dual meshes simultaneously. This paper describe in particular the data structure, an extension of itk::QuadEdgeMesh, a filter to compute and add to the the structure the dual of an existing [...]

Open Source Software to Visualize Complex Data on Remote CEA's Supercomputing Facilities
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In order to guaranty performances of complex systems using numerical simulation, CEA is performing advanced data analysis and scientific visualization with open source software using High Performance Computing (HPC) capability. The diversity of the physics to [...]

Big Data Analysis and Visualization with Open Source Tools
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This talk presents the Open-Source toolkits developed by Kitware for big data analysis.

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 [...]

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 [...]

RGB Image Color Space Transformations
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This paper describes a set of pixel accessors that transform RGB pixel values to a different color space. Accessors for the HSI, XYZ, Yuv, YUV, HSV, Lab, Luv, HSL, CMY, and CMYK color spaces are provided here. This paper is accompanied with source code for [...]

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 [...]

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 [...]

Graph Cuts, <i>Caveat Utilitor</i>, and Euler's Bridges of Konigsberg
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Graph-based algorithms have enjoyed renewed interest for solving computer vision problems. These algorithms have been the subject of intense interest and research. In order to maintain the ITK library au courant, we developed a framework for graph-based [...]

Steps towards the Integration of Model Guided Therapy Systems into the Healthcare Environment
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Hospital Information Systems (HIS) are the primary source of information in clinical routine. In most clinics and medical centers, an electronic health record (EHR) stores relevant patient information which is passed between sub-systems using the ISO standard [...]

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).

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 [...]

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 [...]

Document Object Model based XML Handling in ITK
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The Insight Segmentation and Registration Toolkit (ITK) previously provided a framework for parsing Extensible Markup Language (XML) documents using the Simple API for XML (SAX) framework. While this programming model is memory efficient, it places most of [...]

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, [...]

Walk In A Triangulation : Straight Walk
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This document describes the implementation in ITK of the Straight Walk in a Triangulation algorithm proposed by Devillers et al. Using the exact discrete geometrical orientation predicate, and the itk::QuadEdgeMesh API of ITK, we propose an efficient [...]

Exact Geometrical Predicate: Point in circle
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This document describes the implementation in ITK of the "point in circle" geometrical predicate. Based on Jonathan Shewchuk's work which implements an exact version of the predicate using standard floating point types and arithmetic, the implementation [...]

Enabling ITK-based processing and 3D Slicer MRML scene management in ParaView
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This paper documents on-going work to facilitate ITK-based processing and 3D Slicer scene management in ParaView. We believe this will broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The [...]

The Bag of Words Approach for the Classification of Head and Neck Cancers Using Diffuse Reflectance Spectroscopy
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Diff use Reflectance Spectroscopy (DRS) is a leading technique for the detection of head and neck cancers. It can capture information regarding tissue absorption and scattering. In this research work, we propose a novel method for the identification of normal [...]

The Image-based Vascular Analysis Toolkit (IvanTk)
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This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an [...]

Tubular Geodesics using Oriented Flux: An ITK Implementation
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This document describes an ITK implementation of an interactive method for tracing curvilinear structures. The basic tools provided in this framework are an oriented flux-based tubularity measure and a geodesic path tracer that uses the fast marching [...]

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 [...]

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 [...]

A Spline-Driven Image Slicer
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In this article, a spline driven image slicer algorithm is presented. It is concretized through a vtkAlgorithm-inherited class that takes two inputs and gives two outputs. The first input is the volume from which the slice should reconstructed while 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 [...]

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 [...]

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 [...]

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


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ISSN 2327-770X
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