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optimized image iterators
No opinion
This document describes the iteration direction optimized Image Iterators . Comparing with the original corresponding iterators, the new iterators provide automatic iteration direction optimization and give more flexible. They are more efficient when the [...]

A Quantitative DTI Fiber Tract Analysis Suite
No opinion
Diffusion tensor imaging (DTI) allows a quantitative study of the underlying geometry and architecture of white matter. We have developed a suite of open source tools for quantitative analysis of DTI suitable for use in clinical research studies. We have [...]

FFT Complex to Complex filters and helper classes
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ITK currently supports real to complex conjugate forward and inverse Fourier transformation's through dedicated filters. In turn, these utilize one of a number of Fourier transform implementations, such as that available through VNL, through FFTW or through [...]

Permute Axes Transform for ITK
No opinion
The current ITK release (2.8) already contains a filter that enables permuting coordinate axes of an image: PermuteAxesImageFilter. PermuteAxesTransform provides similar functionality in form if ITK transform. It enables permuting axes as a part of image [...]

Seamless VTK-ITK pipeline connection for image data handling
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Often times developers face the need to connect ITK and VTK pipelines to handle image data. For this purpose, image data importer and exporter classes have been implemented both in ITK and VTK. However, as evident from frequent questions in the ITK and [...]

How to use ITK and MFC
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The object of this application is to illustrate the use of ITK with MFC

Large Image Streaming using ITKv4
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This document illustrates how to process large images (5 and 23 Gigabytes in size) by taking advantage of the streaming capabilities of the Insight Toolkit ITK. Here we illustrate two scenarios: (a) the case when the image itself is larger than the [...]

ComposeRGBA
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This article presents the itk::ComposeRGBAImageFilter.

A generic interpolator for multi-label images
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We present a generic interpolator for label images. The basic idea is to interpolate each label with an ordinary image interpolator, and return the label with the highest value. This is the idea used by the itk::LabelImageGaussianInterpolateImageFunction [...]

ITK Tutorial Presentation Slides
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This course introduces attendees to select open-source efforts in the field of medical image analysis. Opportunities for users and developers are presented. The course particularly focuses on the open-source Insight Toolkit (ITK) for medical image [...]

A MultipleImageIterator for iterating over multiple images simultaneously
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Several applications such as multi-atlas segmentation require frequent iteration over multiple image volumes at the same time. Doing so with the regular ITK iterators is tedious and error prone as it requires updating each iterator at end of each iteration. [...]

Class for Serial Transformations
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This paper describes a simple class for serial transformations, i.e., the concatenation of other transformations. This can be used for doxygen{ResampleImageFilter}.

An ITK Implementation of a Diffusion Tensor Images Resampling Filter
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This paper describes the implementation of a resampling filter for Diffusion Tensor Images (DTI) in the Insight ToolKit (ITK). ITK already contains a filter for resampling scalar and vector images as well as several transformation and interpolation classes. [...]

A Threshold with Hysteresis
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Thresholding is perhaps one of the most basic techniques in image processing. The Insight Toolkit (ITK) includes several threshold filters ranging from simple ones to Otsu based thresholding. Deep into the implementation of the Canny edge detection filter, [...]

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 [...]

An ITK Filter for Bayesian Segmentation:  itkBayesianClassifierImageFilter
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An Insight Toolkit (ITK) filter for image segmentation with applications to brain MRI scans is presented in this paper. Previously, we showed how ITK could be used to implement our algorithm. This paper presents our new ITK filter for Bayesian segmentation [...]

Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems
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This document describes work-in-progress for refactoring ITK’s registration methods to exploit the parallel, computation power of multi-processor, shared-memory systems. Refactoring includes making the methods multi-threaded as well as optimizing the [...]

SharpImage: An Image Processing Prototyping Environment
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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 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 [...]

Polar Transforms for ITK
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Polar transform is a geometric transform, that transforms points form cartesian coordinates to so-called polar coordinates. In case of 2D space, a point in polar coordinate system is addressed by radius and angle. In image processing, polar transform 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
No opinion
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 [...]

Combining Transforms in ITK
No opinion
The current ITK release 2.6 does not contain a way to combine transforms in a structural way. This document describes a contribution to the Insight Toolkit ITK url{www.itk.org}, which implements what we call an doxygen{CombinationTransform}. Two ways to [...]

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, [...]

User-Guided Level Set Segmentation of Anatomical Structures with ITK-SNAP
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Active contour segmentation and its robust implementation using level sets have been studied thoroughly in the medical image analysis literature. Despite the availability of these powerful methods, clinical research still largely relies on manual [...]

The MITK Approach
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The Medical Imaging Interaction Toolkit (MITK) is an opensource toolkit for the development of interactive medical image analysis software. MITK is based on the open-source Insight Toolkit (ITK) and Visualization Toolkit (VTK) and extends them with features [...]

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 [...]

How to use the itk::NaryElevateImageFilter and itk::UnaryRetractImageFilter for the post-processing of medical 4D data
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The subject of the paper is to introduce a new class of 4D filters to itk.While it is very easy to load a 3D volume stored as a series of DICOM images with ITK, some convenience functions that are already available for 3D volumes are not yet available for the [...]

A simple Qt based comparison program for ITK and VTK images.
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This document describes a project that can compare many images simultaneously in a synchronized manner. Such an application can be used in any ITK/VTK image processing pipelines; the programmer can use it to quickly visualize and compare intermediate results [...]

A File Reader for the VisualSonics Vevo 770 Digital RF Data
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A C++ file reader for the VisualSonics Vevo® 770 high frequency ultrasound system is presented. The digital RF header file is read into an XML DOM representation, which can be serialized as XML, HTML, or accessed in C++ natively with data object binding. [...]

Incremental Delaunay Triangulation
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This document describes the implementation in ITK of the Incremental Delaunay Triangulation algorithm. Using the Straight Walk in Triangulation function, the exact discrete geometrical orientation predicate, and the itk::QuadEdgeMesh API of ITK , we propose a [...]

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 [...]

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 [...]

Introduction to ITK Resample In-Place Image Filter
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In this document we present an ITK image filter that outputs a new image with identical voxel contents but with modified physical space representation. The physical space representation of an image is modified to reflect the physical space transform on the [...]

Fast Marching Minimal Path Extraction in ITK
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This paper describes the ITK implementation of a minimal path extraction framework based on Fast Marching arrival functions. The method requires the user to provide three inputs: 1. a meaningful speed function to generate an arrival function, 2. path [...]

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

Conformal Flattening ITK Filter
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This paper describes the Insight Toolkit (ITK) Conformal Flattening filter: itkConformalFlatteningFilter. This ITK filter is an implementation of a paper by Sigurd Angenent, et al., “On the Laplace-Beltrami Operator and Brain Surface Flattening”. This [...]

Integration of Fuzzy Mathematical Morphology and Fuzzy Spatial Relationships into ITK
No opinion
The aim of this paper is to present the integration of new filters computing fuzzy mathematical morphology and spatial relationships into ITK and to share our experience with the Open source community. Our implementation architecture follows the essential [...]

A nonparametric, entropy-minimizing MRI tissue classification algorithm implementation using ITK
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This paper focuses on the role of open-source software in the development of a novel magnetic resonance image (MRI) tissue classification algorithm. Specifically, we describe the of use existing classes in the Insight Segmentation and Registration Toolkit [...]

Segmentation of Skull-infiltrated Tumors Using ITK: Methods and Validation
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Methods for segmentation of skull infiltrated tumors in Computed Tomography (CT) images using Insight Segmentation and Registration Toolkit ITK (www.itk.org) are presented. Pipelines of filters and algorithms from ITK are validated on the basis of [...]

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. [...]

MIPP: A Medical Image Processing Platform based on ITK, VTK and Eclipse RCP
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A novel platform for realizing software prototypes in the area of medical image processing, analysis and visualization is introduced: The "Medical Image Processing Platform" (MIPP). A novel feature is the combination of ITK/VTK with Java/Eclipse RCP, four [...]

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. [...]

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 [...]

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 [...]

Implementation of weighted Dijkstra’s shortest-path algorithm for n-D images
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This paper describes the ITK implementation of a shortest path extraction algorithm based on graph representation of the image and the Dijkstra shortest path algorithm. The method requires the user to provide two inputs: 1. path information in the form of [...]

ITK on the iOS
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ITK is one of the most powerful image segmentation and registration libraries available as an open source toolkit. Motivated by the recent popularization of the iPhone, iPod touch, and iPad, in this work, we describe the set of required steps for integrating [...]

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 [...]

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 [...]

Facet Analyser: ParaView plugin for automated facet detection and measurement of interplanar angles of tomographic objects
No opinion
The presented ParaView plugin allows easy access to the algorithm described in Ref 1. It enables analysis of faceted objects that exhibit distortions in their digital representation, e.g. due to tomographic reconstruction artifacts. The contributed [...]

ITK Image IO interface with Apple iOS
No opinion
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 [...]

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 [...]

N-Dimensional Path Optimization:  The Implementation of a Novel Algorithm in ITK
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Using the path framework we previously added to ITK, we implemented a novel algorithm for n-dimensional path optimization, which we call the ND Swath (NDS). NDS uses dynamic programming to globally optimize the placement of a path within an image, subject to [...]

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 [...]

Creation and Demonstration of a Framework for Handling Paths in ITK
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A hierarchy of path data types and basic path filters were added to ITK, providing a general framework for curves that map a scalar value to a point in n-dimensional space. The framework supports curves that are either continuous (parametric curves) or [...]

A Framework for Algorithm Evaluation and Clinical Application Prototyping using ITK
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The usage of image processing has become an important and continuous growing field in medical imaging. Although a large amount of algorithms is available, only few are routinely applied within applications for clinical diagnosis support and treatment [...]

FusionViewer: An Open Source Toolkit for Viewing Multimodality Images
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FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) [...]

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 [...]

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 [...]

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 [...]

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 [...]

ITK in Biomedical Research and Commercial Applications
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The Insight Segmentation and Registration Toolkit (www.itk.org) has become a standard in academia and industry for medical image analysis. In recent years, the ITK developers' community has focused on providing programming interfaces to ITK from Python, Java, [...]

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 [...]


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