bluuebunny/crossref_metadata_2025 huggingface dataset:
N-Dimensional Computation of Strain Tensor Images in the Insight Toolkit
Authors: Mccormick Matthew
Published: January 2022

Strain quantifies local deformation of a solid body. In medical imaging, strain reflects how tissue deforms under load. Or, it can quantify growth or atrophy of tissue, such as the growth of a tumor. Additionally, strain from the transformation that results from image-to-image registration can be applied as an input to a biomechanical constitutive model.

This document describes N-dimensional computation of strain tensor images in the Insight Toolkit (ITK), www.itk.org. Two filters are described. The first filter computes a strain tensor image from a displacement field image. The second filter computes a strain tensor image from a general spatial transform. In both cases, infinitesimal, Green-Lagrangian, or Eulerian-Almansi strain can be generated.

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. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.
Reproducible Research Training at Scipy 2014
Authors: Ibanez Luis , Mccormick Matthew , Fillon Jean-Christophe , Chaudri Aashish , Nelson Ana , Smith Steve
Published: January 2022

This article illustrates the process of performing reproducible research with existing open source tools.
MPI Read Write
Authors: Hobbs Kevin
Published: January 2022

This paper tests MPI in the Insight Journal testing environment.
UNCHealthyBrainMRI-RView
Authors: Pohl Kilian , Davis Brad , Aylward Stephen
Published: January 2022

BSpline registration results from an application developed by Torsten Rohlfing that is based, in part, on the RView application from Dr. Colin Studholme, Daniel Rueckert, and Julia Schnabel.
Parallel algorithms for erosion and dilation of label images.
Authors: Beare Richard , Jackway Paul
Published: January 2022

It is sometimes useful to be able to apply binary morphological operations, such as erosions and dilations, to labelled images in a fashion that preserves the labels. This article introduces a specialised class implementing parallel methods described in beare et al [2011] that provide very fast dilations by circles and spheres of arbitary size. Comparisons with other implementations using currently available building blocks are also made.
Mattes’ Mutual Information Metric for Multimodality Registration of DESS and T2 Mapped Knee Articular MR Sequences
Authors: Urish Kenneth
Published: January 2022

Registration of multiple MR sequences remains a challenging problem. The Insight Toolkit (ITK) implements the Mattes’ mutual information metric for multimodality registration. Here, example source code, data, and executable files to implement the Mattes’ mutual information metric in ITK are provided. Multiple MR sequences of the knee are used as example images. This serves as a companion manuscript for a permanent archive of the source code, executable file and example data and results.
An ITK Class that Splits Multi-Component Images
Authors: Mccormick Matthew
Published: January 2022

This document describes the implementation of a class for the Insight Toolkit (ITK) that takes an image with multi-component pixels and outputs a scalar image for each component. This can be useful when examining images of vectors, tensors, etc. This ﬁlter may be easier to use and require fewer pixel visitations than an itk::ImageAdaptor with a similar purpose, but it requires additional memory allocation.
An Adaptive Thresholding Image Filter
Authors: Mosaliganti Kishore , Gelas Arnaud , Megason Sean
Published: January 2022

An Insight Toolkit (ITK) algorithm for adaptively thresholding images is presented in this paper. Currently, the usage of thresholding methods in ITK has made use of global thresholds, confidence connected thresholds and neighborhood strategies. The current work extends these family of filters by setting thresholds adaptively in local image regions. The user is not required to specify seed regions apriori which greatly eases the task of automatic segmentation. The thresholds are determined using Otsu’s minimization of between-class variances in local image regions that are selected randomly throughout the domain. Using non-uniformly sampled thresholds, a continuous function is reconstructed throughout the image domain using a B-Spline approximation algorithm. Hence, the image domain is adaptively sampled by making use of the reconstructed threshold function. Most imaging modalities introduce some intensity inhomogeneities that can be recovered by this method.
N-Dimensional Path Optimization: The Implementation of a Novel Algorithm in ITK
Authors: Galeotti John , Stetten George
Published: January 2022

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 several constraints and a user-supplied merit function. The NDS algorithm is presented in this paper along with a description of how it was implemented using ITK.
Importing Contours from DICOM-RT Structure Sets with ITK4
Authors: Dowling Jason
Published: January 2022

This paper presents code for reading contours from DICOM RT structure set files into binary labels. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image analysis environments (such as ITK). An implementation of RT structure set importing is provided with sample data from a prostate cancer radiotherapy planning volume. This is an update to the 2009 Insight Journal paper “Importing Contours from DICOM-RT Structure Sets” which worked with ITK 3.x and a local GDCM2 install.

Updates: Mar 2013 Now correctly handles holes within structures. Thanks to Sebastian Steger for the code fix.
Creating a 2D Active Shape Model Using itk::ImagePCAShapeModelEstimator
Authors: Durkin John , Miller David , Urish Kenneth
Published: January 2022

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 with the guidance of a shape model. The purpose of this document is to fill the void in the ITK user guide on building active shape models. We describe how to create a 2d active shape model of articular femoral knee cartilage using ITK’s ImagePCAShapeModelEstimator. Sample code and example images are provided for displaying the initial principle components of variation. Shape models built with our code can be used for segmentation with itk::GeodesicActiveContourShapePriorLevelSetImageFilter.
Mesh Similarity Calculator
Authors: Li Wen , Magnotta Vincent
Published: January 2022

This documents is about the filter itkQuadEdgeMeshSimilarityCalculator. It takes inputs of two meshes and gives the similarity of the labels on them in two types of similarity measurements – Dice Similarity and Jaccard Similarity. This paper is accompanied with the source code, input data, parameters and output data that we used for validating the algorithm described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.
Information-Theoretic Directly Manipulated Free-Form Deformation Labeled Point-Set Registration
Authors: Tustison Nicholas J. , Awate Suyash , Gee James
Published: January 2022

Our previous contributions to the ITK community include a generalized B-spline approximation scheme as well as a generalized information-theoretic measure for assessing point-set correspondence known as the Jensen-Havrda-Charvat-Tsallis (JHCT) divergence. In this submission, we combine these two contributions for the registration of labeled point-sets. The transformation model which uses the former contribution is denoted as directly manipulated free-form deformation (DMFFD) and has been used for image registration. The information-theoretic approach described not only eliminates exact cardinality constraints which plague exact landmark matching algorithms, but it also incorporates the local point-set structure into the similarity measure calculation. Although theoretical discussion of these two components is deferred to other venues, the implementation details given in this submission should be adequate for those wishing to use our algorithm. Visualization of results is aided by another of our previous contributions. Additionally, we provide the rudimentary command line parsing classes used in our testing routines which were written in the ITK style and also available to use consistent with the open-source paradigm.
Robust Automatic Threshold Selection
Authors: Lehmann Gaetan
Published: January 2022

Robust Automatic Threshold Selection (RATS) is a fast and noise robust automatic thresholding method based on gradients in the image. The basic idea is to choose the threshold at the intensity where the gradient are the highest.
Image Segmentation: Ventricle Isolation Using Region Growing
Authors: Lajara Julio
Published: January 2022

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 Guide and makes use of the ITK library. This paper is accompanied with all source code, input data, parameters and output data that were originally used in developing the image segmentation application, except where prior laws or agreements prohibit redistribution of such material. The only data subject to not being redistributable was the input file used for testing which was a brain dataset from Kitware’s MIDAS collection named Normal090-T2.mha. The rest of this scientific publication is written in a manner such that it facilitates reproducibility of the reported results.
Vessel Enhancing Diffusion
Authors: Manniesing Rashindra , Viergever Max , Niessen Wiro
Published: January 2022

Recently, an implementation of the Vessel Enhancing Diffusion (VED) algorithm [3] using the Insight Toolkit (ITK) framework [2] has been proposed by Enquobahrie et al.[1]. In this paper we present an alternative implementation, for two reasons. First, in this implementation all the main functionality of the algorithm, including eigensystem, vesselness, tensor calculation and PDE discretization using a forward Euler scheme are now grouped together in one single class. Although this may come at the cost of code-reusability, it improves readibility and enables application specific code optimization. The second reason is the criterion of reproducibility. Source code, test environment and example data of the paper [3] are provided.
Fostering Open Science in Lung Cancer Lesion Sizing with ITK module LSTK
Authors: Liu Xiaoxiao , Helba Brian , Krishnan Karthik , Reynolds Patrick , Mccormick Matthew , Turner Wes , Ibáñez Luis , Yankelevitz David , Avila Rick
Published: January 2022

This document describes the latest efforts in integrating the Lesion Sizing Toolkit (LSTK) into ITK v4 as an external/remote module providing an Open Science dashboard website with a large open image archive of lung cancer CT images for LSTK development and testing.
Including TIFF tags in the MetaDataDictionary
Authors: Beare Richard
Published: January 2022

Tiff images are widely used and domain and instrument specific information is often included in some tags. There isn’t any standard way of making use of this information in ITK at present. This article introduces some minor additions to the ITK tiff reader to include the content of some potentially useful tags in the image MetaDataDictionary, thus enabling domain specific information to be extracted from the tags within an ITK application.
Two Luis Miguel fans walk into a bar in Nagoya ---> (yada, yada, yada) ---> an ITK-implementation of a popular patch-based denoising filter
Authors: Tustison Nicholas J. , Manjon Jose
Published: January 2022

This document describes an ITK implementation of the adaptive patch-based image denoising algorithm described in cite{Manjon:2010aa}. This offering consists of the templated class itkPatchBasedDenoisingImageFilter interfaced through the DenoiseImage program which includes its own interface program. We include a couple of examples.
Probabilistic Tissue Characterization for Ultrasound Images
Authors: Curiale Ariel Hernán , Vegas-Sánchez-Ferrero Gonzalo , Aja-Fernández Santiago
Published: January 2022

This document describes the derivation of the mixture models commonly used in the literature to describe the probabilistic nature of speckle: The Gaussian Mixture Model, the Rayleigh Mixture Model, the Gamma Mixture Model and the Generalized Gamma Mixture Model. New algorithms were implemented using the Insight Toolkit ITK for tissue characterization by means of a mixture model. The source code is composed of a set of reusable ITK filters and classes. In addition to an overview of our implementation, we provide the source code, input data, parameters and output data that the authors used for validating the different probabilistic tissue characterization variants described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.
Primal/Dual Mesh with Application to Triangular/Simplex Mesh and Delaunay/Voronoi
Authors: Irshad Humayun , Rigaud Stephane , Gouaillard Alexandre
Published: January 2022

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 mesh, and an adaptor which let a down- ward pipeline process the dual mesh as if it was a native itk::QuadEdgeMesh. The new data structure, itk::QuadEdgeMeshWithDual, is an extension of the already existing itk::QuadEdgeMesh, which already included by default the due topology, to handle dual geometry as well. Two types of primal meshes have been specifically illustrated: triangular / simplex meshes and Voronoi / Delaunay. A functor mechanism has been implemented to allow for different kind of computation of the dual geometry. This paper is accompanied with the source code and examples.
New Features for MinimumMaximumImageCalculator
Authors: Tamburo Robert
Published: January 2022

New functions are proposed for itkMinimumMaximumImageCalculator. One function allows for excluding pixels of a specified value from the computations. Another function stores all pixel indices of the maximum/minimum value. This paper is accompanied with source code for the filter and test, test images and parameters, and expected output images.
Flux driven medial curve extraction
Authors: Mellado Xavier , Larrabide Ignacio , Hernandez Monica , Frangi Alejandro
Published: January 2022

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 an average outward flux measure to distinguish skeletal points from non-skeletal ones. This information is combined with a topology preserving thinning procedure to obtain the final result. This implementation combines this skeletonisation algorithm with other techniques as described in the paper of Bouix et al. to produce an ITK filter that generates as output the skeleton, as a binary object represented in an image, of the input surface, represented as a distance transform image. In this work is described this medial curve extraction procedure following the ITK philosophy.
Criminisi Inpainting
Authors: Doria David
Published: January 2022

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 structures in the image. This implementation is based on the algorithm described in ``Object Removal by Exemplar-Based Inpainting’’ (Criminisi et. al.).

The code is available here: https://github.com/daviddoria/Inpainting
Support for Streaming the JPEG2000 File Format
Authors: Mosaliganti Kishore , Ibanez Luis , Megason Sean
Published: January 2022

This paper describes our contribution of two new classes to the Insight Toolkit (ITK) community. This includes a base and derived ImageIO class for the JPEG2000 file formats based on the openjpeg-v2 libraries. In the current release of ITK, support for JPEG2000 is absent. Our current implementation of the JPEG2000 supports 2D images (8-bit, 16-bit and RGB) and tiling. The latest code is available in the NAMIC Sandbox SVN repository under the project JPEG2000ImageIO. We include 2D example code and tests in this submission. This code is likely to be integrated into ITKv4 very soon.
An ITK Implementation of a Diffusion Tensor Images Resampling Filter
Authors: Budin Francois , Bouix Sylvain , Shenton Martha , Styner Martin , Oguz Ipek
Published: January 2022

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. However, due to the directional nature of DT images, using the existing classes would result in losing the structural information of the image. We developed a new resampling ﬁlter, speciﬁc to DTI, that preserves the structure by applying a rotation directly on the tensors while performing the transformation of the image. New transformation and interpolator classes have also been implemented to handle tensors correctly. The new transformation classes are based on algorithms described by D.C. Alexander et al. Finally, three ﬁlters have been written to correct symmetric semi-deﬁnite matrices that would no longer be positive after the resampling process and project them into the tensors’ space. In addition, a software based on the new classes has been developed and is provided with this article.
IGSTK: Development Process and Project Management Best Practices for an Open Source Software Toolkit for Image-Guided Surgery Applications
Authors: Gary Kevin , Blake Brian , Aylward Stephen , Jomier Julien , Gobbi David , Kim Hee-su , Avila Rick , Ibanez Luis , Cleary Kevin
Published: January 2022

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 the focus is on concurrent development and fast production over requirements management and quality assurance. The image-guided surgery toolkit (IGSTK) is an open source development project that relies on the collaboration of a skilled and distributed development team, yet addresses a domain that demands managing requirements as well as implementing a high degree of robustness and addressing safety concerns. Due to this unique cross-section of open source technology and the surgical domain, the IGSTK team has developed a set of best practices and requirements techniques to augment commonly applied agile methods. This paper presents the lessons we have learned as we have engaged in the software development process.
Collaborative Development of an open framework for medical simulation
Authors: Cotin Stephane , Neumann Paul , Wu Xunlei , Fonteneau Sylvere , Bensoussan Pierre-Jean , Dequidt Jeremie , Marchal Damien , Grisoni Laurent , Karpf Sylvain
Published: January 2022

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 Alcove group at INRIA, we have investigated the foundations for a more extensive, flexible, and comprehensive framework. In addition, five internationally renowned research groups have contributed to this initiative by converting their algorithms into compatible modules. Although still in its very early developmental phase, the current project illustrates some of the key concepts we believe will enable collaboration and interoperability in Medical Simulation. The main objective of SOFA research is to foster collaboration among research groups. It is our hope that SOFA will simplify the development cycles, reduce production costs, and provide a means to share components through a common interface.
A Wavefront OBJ Writer for VTK
Authors: Doria David
Published: January 2022

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.
Cuberille Implicit Surface Polygonization for ITK
Authors: Mueller Dan
Published: January 2022

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 iso-surface and then quadrilaterals are generated for each face. The original approach is improved by projecting the vertices of each cuberille onto the implicit surface, smoothing the typical block-like resultant mesh. Source code and examples are provided to demonstrate the method.
A MultipleImageIterator for iterating over multiple images simultaneously
Authors: Schaerer Joël
Published: January 2022

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. Failing to do so results in hard to debug errors and crashes. The MultipleImageIterator is a simple wrapper class that tries to make this more convenient.
Histogram-based thresholding - some missing methods
Authors: Beare Richard
Published: January 2022

Using intensity histograms to estimate image thresholds is a long established practice in image processing and image analysis and a wide variety of techniques have been developed. Different techniques are appropriate for different intensity distributions. This article implements a number of standard techniques not currently available in ITK.
The BioImage Suite Datatree Tool: Enabling Flexible Realtime Surgical Visualizations
Authors: DiStasio Marcello , Vives Kenneth , Papademetris Xenophon
Published: January 2022

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 surface objects. This Datatree tool provides abstracted file loading, allowing for interface with databases, as well as multisubject capabilities, other plugins designed for specific image modalities, and an incr Tcl based API, allowing users to extend its functionality with their own plugins.
Surface Mesh Normals Filter
Authors: Gelas Arnaud , Gouaillard Alexandre , Megason Sean
Published: January 2022

We have previously developed a new surface mesh data structure in itk (~). In this document we describe a new filter () to estimate normals for a given triangular surface mesh in this data structure. Here we describe the implementation and use of this filter for calculating normals of a .
Giving streaming and multi-threading capabilities to non-streamable ITK filters
Authors: Michel Julien
Published: January 2022

This document describes a filter able to give streaming and multi-threading capabilities to those filters that can not be easily streamed or multi-threaded. The goal of this document is to explain the implementation of this filter, and how it can be used to turn non-streamable filters to streamble ones. It also describes the testing strategy.
Entropy Image Filter
Authors: Tamburo Robert
Published: January 2022

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 with source code for the filter and test, test images and parameters, and expected output images.
Multi-scale Steerable Phase-Symmetry Filters for ITK
Authors: Hatt Charles
Published: January 2022

We have implemented filters for computing phase symmetry (PS) in ITK using steerable filters computed and applied in the Fourier domain. In some recent publications, phase symmetry has been shown to be a useful pre-processing measure for performing image registration and segmentation. Matlab implementations of the code are currently available, but may be slower than C++ versions and most importantly, do not work with volumetric (3D) data. In this paper we briefly provide background information and list some applications of PS filters from the literature. We then provide instructions and examples of how to use the classes and executables.
Optimal mass transport for deformable registration and warping of 2D images
Authors: Shamir Reuben
Published: January 2022

We implement a warping method which is using the properties of elastic materials to compute the deformation between two images. The proposed elastic registration method incorporates the L2 Kantorovich-Wasserstein distance, also known as the Earth Mover’s Distance (EMD), as a similarity measure. The implemented paper presents an efficient partial differential equation approach for a first-order solution of this problem that is simpler than existing works suggested high-order solutions and is computationally simpler than existing works based on linear programming.

Specifically, we implement the following paper Steven Haker, Lei Zhu, Allen Tannenbaum, and Sigurd Angenent, “Optimal mass transport for registration and warping”, International Journal of Computer Vision, 60(3), p. 225-240, 2004.
Read and Write Support for MevisLab Dicom/Tiff Format
Authors: Manniesing Rashindra
Published: January 2022

MevisLab [2] is a development environment for medical image processing and visualization, which supports the reading and writing of combined dicom/tiff images. In this document we provide the source code (ImageIO factory) for the Insight Toolkit (ITK) framework [4]. This image IO plugin supports 2D, 3D and 4D scalar images.

Note: this class depends on version GDCM 2.0 and above.
A small rework for the Gaussian Derivative Image Function
Authors: Mueller Dan
Published: January 2022

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.
Segmentation of Ventricles in the Brain using Connected Threshold
Authors: Berck S
Published: January 2022

This is an implementation of Connected Threshold Segmentation to isolate ventricles using ITK for the Open Source Software Practice course homework.
Triangular Meshes Delaunay Conforming Filter
Authors: Gelas Arnaud , Gouaillard Alexandre , Megason Sean
Published: January 2022

The is the triangulation of a set of points which maximizes the minimum angle of all angles of the triangles, and thus triangle aspect ratios. So converting a non Delaunay triangulation into a Delaunay triangulation, , improves the all triangle aspect ratios and avoid elongated triangles. Note that combining this filter with usual operations like smoothing will provide a better approximation and a better distribution a triangle aspect ratios. Here this document describes a new filter based on the
n
nD
2
2-manifold mesh data structure available in itk: ~ to produce (planar or surfacic) Delaunay triangulation from any non-Delaunay triangulation by edge flipping, by implementing the edge flipping method decribed in~.
Random Sample Consensus (RANSAC) Algorithm, A Generic Implementation
Authors: Yaniv Ziv
Published: January 2022

The Random Sample Consensus (RANSAC) algorithm for robust parameter value estimation has been applied to a wide variety of parametric entities (e.g. plane, the fundamental matrix). In many implementations the algorithm is tightly integrated with code pertaining to a specific parametric object. In this paper we introduce a generic RANSAC implementation that is independent of the estimated object. Thus, the user is able to ignore outlying data elements potentially found in their input. To illustrate the use of the algorithm we implement the required components for estimating the parameter values of a hyperplane and hypersphere.
Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation
Authors: Li Bo , Bryan Frederick , Landman Bennett
Published: January 2022

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 tailored, automatic multi-step processing pipelines (“layouts”) and rapid prototyping of module development. Since its release, JIST has facilitated substantial neuroimaging research and fulfilled much of its intended goal. However, key weaknesses must be addressed for JIST to more fully realize its potential and become accessible to an even broader community base. Herein, we identify three core challenges facing traditional JIST (JIST-I) and present the solutions in the next generation JIST (JIST-II). First, in response to community demand, we have introduced seamless data visualization; users can now click ‘show this data’ through the program interfaces and avoid the need to locating files on the disk. Second, as JIST is an open-source community effort by-design; any developer may add modules to the distribution and extend existing functionality for release. However, the large number of developers and different use cases introduced instability into the overall JIST-I framework, causing users to freeze on different, incompatible versions of JIST-I, and the JIST community began to fracture. JIST-II addresses the problem of compilation instability by performing continuous integration checks nightly to ensure community implemented changes do not negatively impact overall JIST-II functionality. Third, JIST-II allows developers and users to ensure that functionality is preserved by running functionality checks nightly using the continuous integration framework. With JIST-II, users can submit layout test cases and quality control criteria through a new GUI. These test cases capture all runtime parameters and help to ensure that the module produces results within tolerance, despite changes in the underlying architecture. These three “next generation” improvements increase the fidelity of the JIST framework and enhance utility by allowing researchers to more seamlessly and robustly build, manage, and understand medical image analysis processing pipelines.
How to use the itk::NaryElevateImageFilter and itk::UnaryRetractImageFilter for the post-processing of medical 4D data
Authors: Roettger Stefan
Published: January 2022

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 4D case. Especially for MR data (and to a certain limit also for CT data) it is very important to look at the full 4D series, since the radiologist usually does not make a diagnosis based on a single volume but on the full time series of volumes which shows the temporal flow of the contrast agent. As an example, for breast imaging the radiologist typically examines parameter maps like MIPt (maximum intensity over time), TTP (time to peak) or WI (Wash-In). These parameter maps are the 3D result of post-processing the entire 4D time series. The goal of proposing the denoted 4D filters is to provide ITK with functionality that enables a postprocessing job to handle the entire 4D series as one entity and not as a loose collection of 3D volumes.
A DICOM-based Software Infrastructure for Data Archiving
Authors: Dalal Dhaval , Jomier Julien , Aylward Stephen
Published: January 2022

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 (www.dspace.org), an open-source web-based digital library technology. We have extended and linked existing, freely-available DICOM and digital library software to create DICOM Accessible Digital Libraries (DADLs). Specifically, DICOM objects (and other medical image data formats such at Analyze,MetaImage) uploaded to a DADL can be grouped with other files such as journal articles or tracker data, viewed as thumbnails, and made publicly or privately available for others to search and download from a linked DICOM server. In that manner, once a researcher has identified the data he / she needs via an Internet search using meaningful descriptors, the data can be directly downloaded via standard DICOM query and retrieve utilities and that data will be perpetually indexed and accessible via an Internet handle.
3D Voxel-Based Volumetric Image Registration with Volume-View Guidance
Authors: Li George , Xie Huchen , Ning Holly , Citrin Deborah , Copala Jacek , Arora Barbara , Coleman Norman , Camphausen Kevin , Miller Robert
Published: January 2022

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 any given anatomic landmark, usually the skin/muscle voxels. This registration criterion has been validated using two different approaches, including comparison with automatic registration using mutual information based on the Insight Toolkits (ITK) and comparison with registered MR images with different pulse sequences acquired directly from the same MR scanner less than 5 minutes. An investigation is also made to compare this technique with the conventional interactive image registration using three orthogonal planar (3P) views, which is predominantly used in the current treatment planning in clinic. This 3D technique has shown several advantages, including improved registration accuracy and accelerated registration speed. It has also found that the 3P pixel registration technique often “inherits” a global positioning error, due to its partial 3D visual presentation. In addition, unlike the 3P technique, which generally cannot be used to register more than 2 images simultaneously and low resolution PET images, this 3D technique can register up to 4 imaging modalities simultaneously, including PET images, with both global view guidance and detail checking capability.
MINC2.0 IO Support for ITK
Authors: Baghdadi Leila
Published: January 2022

MINC2.0 IO support for ITK.
Introduction to ITK Resample In-Place Image Filter
Authors: Lu Wei , Johnson Hans
Published: January 2022

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 input image. The advantage of this filter is that it is free from interpolation error. This paper is accompanied with the source code, input data, parameters and output data that the au- thors used for validating the algorithm described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.
Well-Composedness and the Topological Repairing of 2-D and 3-D Digital Images
Authors: Tustison Nicholas J. , Siqueira Marcelo , Gee James
Published: January 2022

In an earlier submission, we considered 2-D and 3-D digital binary images topologically characterized by their well-composedness. Well-composed images exhibit important topological and geometrical properties not shared by their ill-composed counterparts. These properties have important implications for various algorithms used by the ITK community such as thinning algorithms and Marching Cubes.

A natural follow-up inquiry to our original submission concerns the possible extension of the binary algorithm to accommodate images with multiple labels. In this paper, we describe such a generalization of our previous submission which also subsumes the binary approach. For completeness and clarity of exposition, we develop the idea of well-composedness within the binary image context and later generalize the discussion to include those images with multiple labels.
A new implementation of itk::ImageToImageFilter for efficient parallelization of image processing algorithms using Intel Threading Building Blocks
Authors: Jaberzadeh Amir , Scherrer Benoit , Warfield Simon
Published: January 2022

Modern medical imaging makes use of high performance computing to accelerate image acquisition, image reconstruction, image visualization and image analysis. Software libraries that provide implementations of key medical imaging algorithms need to efficiently exploit modern CPU architectures. In particular, workstations with small numbers of cores are being replaced by very high core count architectures, and by many integrated core architectures, which offer acceleration by vectorization and multi-threading.

The Insight Toolkit (ITK) is the premier open source implementation of medical imaging algorithms, with a generic design for image processing filters that allows for many developers to rapidly incorporate these algorithms in to new applications. While ITK filters benefit from a generic, platform independent multithreading capability, the current implementation is difficult to exploit to achieve very high performance. Specifically, ITK relies on a static decomposition of the image into subsets of equal size which can be highly inefficient. Threads that terminate early due to uneven work throughout the image finish early and do not contribute further to the processing of more complex regions, leading to idle computational resources and longer execution times. Performance is also difficult to coordinate across multiple algorithms, as the ITK filter assumes each filter operates independently but the global implementation has an impact across filters.

In this work, we propose a novel, simple to use, high performance multithreading capability for ITK that accelerates the itk::ImageToImageFilter. We utilise a workpile data decomposition strategy, and leave the task of optimal job scheduling on CPU cores to the library called Threading Building Blocks (TBB). We demonstrate the efficacy of multi-threading with TBB in comparison to the itk::Multithreader class, through three simple example image analysis algorithms.

Our implementation provides a new multi-threaded itk::ImageToImageFilter that can be conveniently reused to provide simple and efficient multi-threaded code across applications and algorithm libraries. Our new implementation is distributed as open-source software to the community and is straightforward to adopt.
ITK Mesh IO Framework
Authors: Zhu Wanlin
Published: January 2022

ITK has a powerful and flexible image IO framework. Reading and writing different types of image file is straightforward. The image IO could be easily extended by writing a specific image IO class for a new image file format. Whereas, there is no such framework for easily reading and writing itk::Mesh/itk::QuadEdgeMesh, At the moment, only a few specific classes to read vtk polydata format and is not easily to be extended. This paper describes our contribution to itk for providing a mesh IO framework which could be used for reading and writing some commonly used mesh file formats. The mesh IO classes worked well for both itk::Mesh and itk::QuadEdgeMesh.
Stochastic Fractal Dimension Image
Authors: Tustison Nicholas J. , Gee James
Published: January 2022

Fractal analysis for medical image classification and analysis was introduced in cite{Chen1989}. According to the authors, when viewed as an intensity surface, Mandelbrot's fractal theory provides an informative framework for characterizing such a surface. Using the fractional Brownian motion model, the authors provide an algorithm for converting a scalar image to a fractal dimension image for classification purposes or edge enhancement. This submission constitutes a report on the ITK implementation of this algorithm.
Warp Mesh Filter
Authors: Li Wen , Magnotta Vincent
Published: January 2022

This documents is about the filter itk::WarpQuadEdgeMeshFilter. It takes two input meshes (fixed and moving meshes) and one deformation field. It produces one output mesh. Each point on the fixed mesh is warped according to the displacement vector saved in the deformation field and gets a scalar value assigned by interpolating the scalar value from the moving mesh. An interpolator is needed to apply this filter. This paper is accompanied with the source code, input data, parameters and output data that we used for validating the algorithm described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.
Radial Thickness Calculation and Visualization for Volumetric Layers
Authors: Wang Defeng , Shi Lin , Heng Pheng Ann
Published: January 2022

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 several definitions for the layer thickness. A newly proposed thickness definition is the radial thickness, which is defined as the distance between each pair of corresponding points on the two surfaces with the same polar coordinate. The thickness values calculated by the radial thickness definition are unique and does not depend on the starting surface. In this paper, we describe a class for calculating the radial thickness of one volumetric layer represented as coupled and nested triangle meshes.

The class, vtkRadialThicknessCalculate, is implemented using the Visualization Toolkit (VTK). In this document, we describe the radial thickness calculation algorithm and provide the user with the source code and the input data to reproduce the results. The radial thickness calculation described in this paper has a variety of applications including the thickness calculation for the skull vault, which is the original motivation for this work.
Improving The Oriented Image Class For Use In The Registration Framework
Authors: Brooks Rupert , Arbel Tal
Published: January 2022

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 gradient calculations. Furthermore, general code that uses the itk::OrientedImage will suffer an unnecessary penalty when the image is oriented parallel to the image axes. We propose a new itk::FastOrientedImage class that alleviates these performance problems, and a change to the design of itk::ImageToImageMetric that resolves the gradient issue, and adds a number of additional capacities to the image metrics
Clustering Based Cardiac Resynchronization Therapy Prediction using Open Source Toolkit PRTools
Authors: Huang Heng , Shen Li , Zhang Rong , Makedon Fillia , Pearlman Justin
Published: January 2022

We propose a novel framework at MICCAI 2005 to predict pacing sites in the left ventricle (LV) of a heart. This framework can be used to assist pacemaker implantation and programming in cardiac resynchronization therapy (CRT) that is a widely adopted therapy for heart failure patients. Hierarchical agglomerative clustering technique is performed to the time series of LV wall thickness to identify pacing site candidates. Meanwhile, pearson correlation coefficients of wall motion series show the dissimilarity between them. These main components of our clustering based prediction framework are implemented by using open source software toolkit PRTools.
Exponentiation Filters
Authors: Lehmann Gaetan
Published: January 2022

Two simple filters are contributed to compute the exponential of an image: the first one to raise the image to the power of a constant, the other one to raise the image to the power of the values provided in another image.
ContourExtractor2DImageFilter: A subpixel-precision image isocontour extraction filter.
Authors: Pincus Zachary
Published: January 2022

This document describes itk::ContourExtractor2DImageFilter, an implementation of the arching squares2D contour-finding method using the Insight Toolkit ITK www.itk.org. This filter takes as input a 2D image (not necessarily binarized) and a contour value, and outputs zero or more itk::PolyLineParametricPath objects which represent the image contours at that value.
UNCHealthyBrainMRI-RegisterImagesModule
Authors: Aylward Stephen , Ibanez Luis , Turek Matt , Davis Brad , Kikinis Ron
Published: January 2022

UNCHealthBrainMRI registration test results from the RegisterImagesModule that is distributed with Slicer and via KWPublic.
CITK - an architecture and examples of CUDA enabled ITK filters
Authors: Beare Richard , Micevski Daniel , Share Chris , Parkinson Luke , Ward Phillip , Goscinski Wojtek , Kuiper Mike
Published: January 2022

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 been under investigation for a number of years. This article describes modifications to the InsightToolkit (ITK) that provide a simple architecture for transparent use of GPU enabled filters and examples of how to write GPU enabled filters using the NVIDIA CUDA tools.

This work was performed between late 2009 and early 2010 and is being published as modifications to ITK 3.20. It is hoped that publication will help inform development of more general GPU support in ITK 4.0 and facilitate experimentation by users requiring functionality of 3.20 or wishing to pursue CUDA based developments.
ImageLinearIterator - WithIndex removed
Authors: Beare Richard
Published: January 2022

ITK includes a number of iterators including the {} and {} that support visiting voxels along lines parallel to the image axes. This is particularly useful for separable filters. This article introduces modified versions that do not maintain location index so that filters that don’t require index information can perform faster.

Preliminary tests indicate that the iteration speed is improved, but that filters such as the RecursiveSmoothingGaussianImageFilter do not change significantly.