bluuebunny/crossref_metadata_2025 huggingface dataset:
New Expectation Maximization Segmentation Pipeline in Slicer 3
Authors: Rannou Nicolas , Jaume Sylvain , Pieper Steve , Kikinis Ron
Published: January 2022

Many neuroanatomy studies rely on brain tissue segmentation in Magnetic Resonance images (MRI). The Expectation-Maximization (EM) theory offers a popular framework for this task. We studied the EM algorithm developed at the Surgical Planning Laboratory (SPL) at Harvard Medical School and implemented in the Slicer3 software. We observed that the segmentation lacks accuracy if the image exhibits some intensity inhomogeneity. Moreover the optimum parameters are challenging to estimate. This document aims at describing our solutions within the context of statistical modeling. Our contributions range from algorithm improvements to novel representations of the statistical distribution model. First we added a bias field correction module and exposed the most significant parameters. Second we proposed a new way to select the distribution of the tissues to be segmented. Finally we designed a set of interactive tools to make the segmentation process easier and more accurate. To validate the new segmentation pipeline, we performed our experiments on MRI data and a clinical expert evaluated our results.

The source code developed for this work, i.e. the code of the MRIBiasFieldCorrection and EMSegment modules, is part of Slicer3 version 3.5 and can be downloaded by this command: svn co http://svn.slicer.org/Slicer3/trunk Slicer3
GPU Volume Ray Casting of two Volumes within VTK
Authors: Krissian Karl , Falcón-Torres Carlos
Published: January 2022

We have modified the current VTK volume rendering on GPU to allow simultaneous rendering of two volumes, each of them with its own color and opacity transfer functions. These changes have led to the creation of two new C++ classes and several GLSL shaders. We explain the modifications made to the original classes and shaders and we discuss possible additional improvements. A C++ demo code shows how to use the new classes.
Interactive Image Graph Cut Segmentation
Authors: Doria David , Chen Siqi
Published: January 2022

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 Insight Toolkit. The graph cut function itself is the maxflow-v2.21 algorithm written by Yuri Boykov and Vladimir Kolmogorov. This version of their algorithm is released under a GPL license.

The code for this paper can be found here: https://github.com/daviddoria/InteractiveImageGraphCutSegmentation/commit/259cd239169c5ea8c44cc68908886eca10cc8239

Updates will be published here: https://github.com/daviddoria/InteractiveImageGraphCutSegmentation

Note: You must use the latest git version of VTK as of the date of this publication to avoid compiler errors due to newly added functions.
Optimization of connected component labelling
Authors: Beare Richard
Published: January 2022

The report details some modifications made to the ITK {} in an attempt to improve performance. Some interesting observations were made during this process. A new filter using a different algorithm to perform the same function is also described and improved performance demonstrated.
Incremental Delaunay Triangulation
Authors: Rigaud Stephane , Gouaillard Alexandre
Published: January 2022

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 geometrically exact and robust implementation that, from a given 2-dimensional itk::PointSet, incrementally constructs the corresponding 2-dimensional Delaunay Triangulation as an itk::QuadEdgeMesh.
Improving features and performance of binary erode and dilate filters
Authors: Lehmann Gaetan
Published: January 2022

Binary erosion and dilation are the base filters of binary mathematical morphology. In ITK 2.4.1 and implement an efficient algorithm described in . However, those filter lack support for boundary values, have a poor progress report, and can be quite inefficient for complex 3D images.
A GPU-based Implementation of Multimodal Deformable Image Registration Based on Mutual Information or Bhattacharyya Distance
Authors: Lou Yifei , Jia Xun , Gu Xuejun , Tannenbaum Allen
Published: January 2022

This paper describes a multimodal deformable image registration method on the GPU. It is a CUDA-based implementation of a paper by E. D’Agostino et. al, ‘’A viscous fluid model for multimodal non-rigid image registration using mutual information’’. In addition, we incorporate an alternative metric as opposed to mutual information, called Bhattacharyya Distance, in the recent work of Lou and Tannenbaum. This paper is accompanied with the source code, input data, parameters and output data that the authors used for validating the algorithm.
Generalized Computation of Gaussian Derivatives Using ITK
Authors: Macia Ivan
Published: January 2022

Computation of local image derivatives is an important operation in many image processing tasks that involve feature detection and extraction, such as edges, corners or more complicated features. However, derivative computation in discrete images is an ill-posed problem and derivative operators without any prior smoothing are known to enhance noise. Here we present a new convolution operator, the GaussianDerivativeOperator, that allows to calculate locally Gaussian derivatives of N order. Furthermore, we present some useful classes and examples that make use of this new operator.
Conformal Flattening ITK Filter
Authors: Gao Yi , Melonakos John , Melonakos John , Tannenbaum Allen
Published: January 2022

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 filter performs an angle preserving map of any genus zero (i.e. no handles) triangulated mesh to the sphere or, alternatively, to the plane. In other words, any given triangle in the resulting sphere will have the same angles as the corresponding triangle in the original mesh, though their areas may differ. In this paper, we describe our code and provide the user with enough details to reproduce the results which we present in this paper. This filter has a variety of applications including the flattening of brain surfaces, which was the initial motivation for this work.
Improving performance of morphological reconstruction
Authors: Beare Richard
Published: January 2022

Morphological reconstruction may be implemented in a number of different ways. ITK has an iterative method and a non iterative method. This article compares the performance of another non iterative method and finds a significant improvement.
Gaussian Interpolation
Authors: Yushkevich Paul , Tustison Nicholas J. , Gee James
Published: January 2022

In this submission, we offer the GaussianInterpolationImageFunction which adds to the growing collection of existing interpolation algorithms in ITK for resampling scalar images such as the LinearInterpolateImageFunction, BSplineInterpolateImageFunction, and WindowedSincInterpolateImageFunction. We provide a brief discussion of the theory behind the submission and the algorithmic implementation.
Creation and Demonstration of a Framework for Handling Paths in ITK
Authors: Galeotti John , Stetten George
Published: January 2022

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 discrete (chain-codes). Example usage of the entire framework is demonstrated using a previously published 2D active contour algorithm that was converted to ITK.
A nonparametric, entropy-minimizing MRI tissue classification algorithm implementation using ITK
Authors: Tasdizen Tolga , Awate Suyash , Whitaker Ross
Published: January 2022

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 (ITK) and several new classes that were implemented to perform non-parametric density estimation and entropy minimization. These new classes also provide a general framework for nonparametric density estimation and related applications.
A generic interpolator for multi-label images
Authors: Schaerer Joël , Roche Florent , Belaroussi Boubakeur
Published: January 2022

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 interpolator. Unfortunately, this class is currently limited to Gaussian interpolation. Using generic programming, our proposed interpolator extends this idea to any image interpolator. Combined with linear interpolation, this results in similar or better accuracy and much improved computation speeds on a test image.
Importing Contours from DICOM-RT Structure Sets
Authors: Dowling Jason , Malaterre Mathieu , Greer Peter B , Salvado Olivier
Published: January 2022

This paper presents parsing software for importing contours from DICOM RT structure set files into binary image files. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image analysis environments (such as ITK). We provide an implementation of RT structure set importing and give some example results from prostate cancer radiotherapy planning volumes.

Please note that this implementation requires GDCM 2.0 to be installed (this is trivial; however this requirement is the reason for the low automatic testing score by the Insight-Journal Dashboard).

Please Note: Updated June 2010 for a couple of minor issues (pls. see comments in .cxx) and to remove the requirement for image template. This code now reads the dcm directory and creates a 3D volume and associated binary structure volumes (all in NIfTI format). Usage: itkDICOMRT DicomDirectory inputDICOMRTImageFile OutputFilePrefix

Feb 2013: Please note that this code won’t work with ITK4 and above - instead please see: http://hdl.handle.net/10380/3401 . There is also a new test DICOM-RT directory with that paper.

Mar 2013 Now correctly handles holes within structures. Thanks to Sebastian Steger for the code fix.
itkLocalMaximaImageFilter
Authors: Lloyd Bryn , Szekely Gabor , Warfield Simon
Published: January 2022

This filter finds the local maxima of an image. The result is returned as a PointSet. Additionally a binary image, with 0 for background, and 1 for the points can be retrieved.
Automatic Junction Detection for Tubular Structures
Authors: Xiong Guanglei , Xing Lei , Taylor Charles
Published: January 2022

Junctions of tubular structures (vasculature, trachea, neuron, etc) in medical images are critical for the topology of these structures. Identification of them is helpful in many applications. For example, quantification of geometric vascular features, registration of trachea movement due to respiration, tracing of neuron path. However, manual extraction of junctions can be tedious, time-consuming, and subject to operator bias. In this paper, we propose a novel method to detect them automatically and describe how to implement it in ITK framework. The input is a 2D/3D binary image that can be obtained from any segmentation techniques. The output will be positions of junctions and their sizes. There are only two parameters which need to be set by the user. We provide here the implementation as a ITK class: itk::JunctionDetectionFilter. Please cite the following paper if you are interested in our work. G. Xiong, C. Chen, J. Chen, Y. Xie, and L. Xing, Tracking the Motion Trajectories of Junction Structures in 4D CT Images of the Lung, Vol. 57, No. 15, pp. 4905-4930, Physics in Medicine and Biology, 2012.
Extracting Intersections of Coplanar Surfaces (Boolean-operation on touching meshes)
Authors: Grothausmann Roman
Published: January 2022

The contribution to VTK presented in this article is specialized on the extraction of contact surfaces (CS). This extraction can be regarded as the intersection Boolean-operation of only touching meshes. The vtkCoplanarSurfaceExtractor filter produces either polygonal or triangulated CSs by reconstructing the contact faces of co-planar triangles. Specified tolerances account for discrepancies in coplanarity of faces which might occur due to rounding effects. This article is accompanied with the source code, input data, parameters and output data that were used for validating the VTK-filter.
Integration of the Java Image Science Toolkit with E-Science Platform
Authors: Damon Stephen , Panjwani Sahil , Bao Shunxing , Kochunov Peter , Landman Bennett
Published: January 2022

Medical image analyses rely on diverse software packages assembled into a “pipeline”. The Java Image Science Toolkit (JIST) has served as a standalone plugin into the Medical Image Processing Analysis and Visualization (MIPAV). We addressed shortcomings that previously prevented deeper integration of JIST with other E-science platforms. First, we developed an interface for integrating externally compiled packages (similar to the interfaces in NiPy) such that the application can become a “draggable module” in the module tree. This allows for connection of inputs and outputs to other JIST modules while maintaining external processing and monitoring. Second, we develop an integration interface with the Neuroimaging Informatics Tools and Resources Clearinghouse Cloud Environment (NITRC-CE). User can launch and terminate pre-configured nodes to utilize computational resources of the Amazon cloud. Finally, we define a new external data source, which can connect to the eXtensible Neuroimaging Archive Toolkit (XNAT) to query and retrieve remote data using XNAT’s REST API. Specifically, we define dataflow for files that can readily be converted into volumes and collections of volumes to interface with any JIST module that expects volumetric image data as an input. Users now have the ability to run their pipelines from a well-defined external data source and no longer are required to already have data on the disk. With these upgrades we have extended JIST’s capabilities outside of complied java source code and enhanced capabilities to seamlessly interface with E-science platforms.
An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open-source software
Authors: Pace Danielle , Kikinis Ron , Hata Nobuhiko
Published: January 2022

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 medical image processing). The tutorial covers all stages of a typical IGT or medical robotics procedure, including the concepts of imaging, preoperative planning, targeting and tracking, navigation and registration, by using the LEGO robot to perform a “needle biopsy” on a phantom (anatomical model) made of traditional LEGO pieces. In addition, this paper describes a C++ library that allows direct control of a LEGO Mindstorms NXT robot from a Linux computer over a USB connection.
A Mean Shift Clustering Implementation for VTK
Authors: Doria David
Published: January 2022

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 hosted at http://github.com/daviddoria/vtkMeanShiftClustering .
SharpImage: An Image Processing Prototyping Environment
Authors: Mueller Dan
Published: January 2022

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. The user interacts with the environment using a command console, and can view images as a series of slices or through volume rendering. We describe the design and introduce functionality using a number of examples. We have found the environment useful for prototyping a range of image processing tasks and provide the source-code in the hope others may also find it useful.
Implementation of graph-based interactive 3D vessel segmentation filter
Authors: Pellow David , Freiman Mot , Joskowicz Leo
Published: January 2022

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 based segmentation of the vessel based on the intensity information coupled with the computed path as a spatial constraint. The shortest path computation is adapted from the algorithm in [1] to use a vesselness based weighting function. The min-cut algorithm uses the Boost graph library to calculate the minimal cut. Several examples of applications are provided, along with images of the resulting segmentations.
MathVisionTools: mathematical prototyping in medical image analysis
Authors: Van almsick Markus , Ter haar romeny Bart , Bennink Edwin H.
Published: January 2022

Medical image analysis today is based on serious mathematics. More and more methods involve PDE’s, linear algebra, complex transforms, optimization theory etc. This paper introduces the software environment MathVisionTools that is suited for the design stage, where the emphasis lies on mathematical modeling. MathVisionTools is written in the high level language Mathematica.
Iterative Smoothing of Field Data in Spherical Meshes
Authors: Ibanez Luis , Yeo B.t. thomas , Golland Polina
Published: January 2022

This document describes a contribution to the Insight Toolkit intended to smooth the values of Field data associated with the nodes of a Spherical Mesh. The Mesh Smoothing filters contributed here do not modify the geometry or the topology of the Mesh. They act only upon the pixel data values associated with the nodes. Two filters are presented, one that smooths scalar field data, and a second one that smooths vector field data. 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.
Voxel Value Ratio Variance Image Registration Metric for the Insight Toolkit
Authors: Topping Geoff
Published: January 2022

This document describes a cost function, or metric, for use in image registration using the Insight Toolkit. The RatioVarianceImageToImageMetric class implements a metric which is calculated from the variance of the ratios of voxel values of the moving and fixed images.
A Novel Information-Theoretic Point-Set Measure Based on the Jensen-Havrda-Charvat-Tsallis Divergence
Authors: Tustison Nicholas J. , Awate Suyash , Gee James
Published: January 2022

A novel point-set registration algorithm was proposed in [6] based on minimization of the Jensen-Shannon divergence. In this contribution, we generalize this Jensen-Shannon divergence point-set measure framework to the Jensen-Havrda-Charvat-Tsallis divergence. This generalization permits a ﬁne-tuning of the actual divergence measure between robustness and speciﬁcity. The principle contribution of this submission is theitk::JensenHavrdaCharvatTsallisPointSetMetric class which is derived from the existing itk::PointSetToPointSetMetric. In addition, we provide other classes with utility that would extend beyond the point-set measure framework that we provide in this paper. This includes a point-set analogue of the itk::ImageFunction, i.e. itk::PointSetFunction. From this class we derive the class itk::ManifoldParzenWindowsPointSetFunction which provides a Parzen windowing scheme for learning the local structure of point-sets. Finally, we include the itk::DecomposeTensorFunction class which wraps the different vnl matrix decomposition schemes for easy use within ITK.
Confidence Connected Segmentation of the Lateral Ventricles
Authors: Radin Philip
Published: January 2022

In this paper we attempt to segment the lateral ventricles using the ITK provided Confidence Connected algorithm. An ITK application was used to explore the various input parameters to produce an image of acceptable presentation. Input MRI data of healthy individual was provided through the MIDAS repository resulting in a segmented image.
JPEG 2000 in Medical Applications
Authors: Malaterre Mathieu
Published: January 2022

The DICOM Working Group 4 (compression group) has approved in November 2001 the use of JPEG 2000 compression as part of the DICOM standard. This document describes how this wavelet transform-based image compression algorithms is now integrated via GDCM and OpenJPEG in the Insight Toolkit ITK.
Image Segmentation
Authors: OConnor Kayleigh
Published: January 2022

This document describes an algorithm implemented using the Insight Toolkit ITK www.itk.org. This paper is accompanied with the source code, input data, parameters and output data that the authors used for validating the algorithm described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.
A Leica PTX Reader for VTK
Authors: Doria David
Published: January 2022

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.
A Label Geometry Image Filter for Multiple Object Measurement
Authors: Padfield Dirk , Miller James
Published: January 2022

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 filters measure features of labeled masks. It differs, however, in that it measures geometric features of the objects themselves rather than statistics of image intensities under the masks defined by the objects. This document describes the mathematical background of the geometric features measured by this filter and describes the framework of the code, which is structured to enable easy expandability as new object features are desired.
Poisson Editing in ITK
Authors: Doria David
Published: January 2022

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 smooth as possible. We also explain how these techniques can be used to reconstruct an image after perform editing operations in the gradient domain.

The code is available here: https://github.com/daviddoria/PoissonEditing
OpenCL accelerated GPU binary morphology image filters for ITK
Authors: Bardosi Zoltan
Published: January 2022

Binary morphological operations are fundamental tools in image processing but the processing time scales with the number of pixels thus making them expensive operations on the CPU for larger 3D datasets that typically appear in medical imaging. Since erosion and dilatation are special neighborhood operators, each pixel in the output depends only on the neighborhood region which makes them fit for massive GPU parallelization. This document introduces a new ITK module that implements generic (OpenCL based) GPU accelerated binary morphology image filters for erosion and dilatation. The filter can be executed within the standard ITKGPU pipeline.
An Empirical Optimization to Logistic Classification Model
Authors: Senra Filho Antonio Carlos da Silva
Published: January 2022

Recently, the scientific community has been proposing several automatic algorithms to biomedical image segmentation procedure, being an interesting and helpful approach to assist both technicians and radiologists in this time-consuming and subjective task. One of these interesting and widely used image segmentation method could be the voxel intensity-based algorithms, e.g. image histogram threshold methods, which have been intensively improved in the past decades. Recently, an interesting approach that gained focus is the logistic classification (LC) for object detection in biomedical images. Even though the general concept behind the LC method is fairly known, the proper method’s optimization still commonly adjusted by hand which naturally adds a level of uncertainty and subjectivity in the general segmentation performance. Therefore, an empirical LC optimization is presented, offering a ITK class that performs the LC parameters optimization based on empirical input data analysis. It is worth mentioning that the LogisticContrastEnhancementImageFilter class showed here is also applied on others computational problems, being briefly explained in this document.
An Architecture Validation Toolset for Ensuring Patient Safety in an Open Source Software Toolkit for Image-Guided Surgery Applications
Authors: Gary Kevin , Kokoori Shylaja , David Beulah , Otoom Mwaffaq , Blake M. brian , Cleary Kevin
Published: January 2022

As open source software projects gain acceptance in mission critical domains of a technology-enabled society, they must adapt their lightweight processes and tools to address the quality needs of these domains. One such domain is technology-supported surgical interventions. This paper presents an in-development toolset for validating the architecture of the open source Image-guided Surgical Toolkit (IGSTK). IGSTK components must conform to a specific architecture pattern based on state machines. Applications built on top of the IGSTK framework process and route instructions under specific constraints imposed by the architecture. This toolset focuses on validating that component state machines in IGSTK are designed and implemented in accordance with the architecture’s constraints. These tools employ open source components as well, and apply theoretical concepts from computer science to a practical problem of guaranteeing safety in a mission critical domain.
Alternative Memory Models for ITK Images
Authors: Mueller Dan
Published: January 2022

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 document describes three alternative memory models: slice contiguous, sparse, and single-bit binary images. Slice contiguous images are three-dimensional images, in which each slice is stored in a contiguous 1-D array, but the slices are not necessarily adjacent in memory. Slice contiguous images are well suited for interoperability with applications representing images using DICOM. Sparse images are n-dimensional images, in which each pixel is stored in a hash table data structure. This memory model is well suited for images with very large dimensions, but few pixels which are actually relevant. Single-bit binary images internally represent each pixel as a single-bit, in contrast to eight-bits required to represent a boolean. Single-bit binary images allow very compact representations for on-off masks. Source code, tests, and examples are provided to allow easy reproduction and use.
Hough Transform Plane Detector
Authors: Borrmann Dorit , Doria David
Published: January 2022

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.
A K-Means++ Clustering Implementation for VTK
Authors: Doria David
Published: January 2022

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 finds the global optimum much more frequently than a naive/random initialization.

The code is currently hosted at http://github.com/daviddoria/KMeansClustering .
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy
Authors: Vercauteren Tom , Pennec Xavier , Perchant Aymeric , Ayache Nicholas
Published: January 2022

This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion’s demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver framework. We show that this framework can be extended to handle diffeomorphic transformations. The source code is composed of a set of reusable ITK filters and classes. In addition to an overview of our implementation, we provide a small example program that allows the user to compare the different variants of the demons algorithm.
Simulated Diffusion-Weighted Imaging for the ITK Masses
Authors: Tustison Nicholas J. , Cook Philip , Avants Brian , Stone James
Published: January 2022

A recent article by Van Hecke et al. [3] describes a framework for creating simulated diffusion-weighted images (DWI). The methodology allows for modeling intersubject variability, regional pathology, and noise and is quite useful for evaluation purposes. This article describes our ITK implementation of this work which we provide to the community as open source.
LookAt Transform Initializer and Oblique Section Image Filter
Authors: Mueller Dan
Published: January 2022

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 transform can also be used to obtain an oblique section: a single arbitrary 2-D slice through a 3-D image.
Triangle Mesh Subdivision
Authors: Zhu Wanlin
Published: January 2022

This document describes a contribution to the Insight Toolkit intended to support the process of subdivision of triangle mesh. Four approaches, linear, Loop, modified butterfly andsqrt{3}sqrt3subdivision schemes were introduced.
Distributed Anisotropic Diffusion
Authors: Hobbs Kevin
Published: January 2022

Distributed anisotropic diffusion provides a wrapper program around ITK’s anisotropic diffusion filters that allows an input image to be spread across the memory of several computers and the processors of all of the computers to work simultaneously on the output. Distributed anisotropic diffusion allows the Visible Woman Head dataset to be smoothed with 100 iterations of the vector gradient magnitude anisotropic diffusion filter in 47 minutes on an 8 node 64 core cluster versus 53 minutes for just 10 iterations of standard vector gradient magnitude anisotropic diffusion on a single node.
Adding Refined Isosurface Rendering and Shadow Mapping to vtkGPUVolumeRayCastMapper
Authors: Herrera Imanol , Buchart Carlos , Borro Diego
Published: January 2022

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 the users immersion as well as its depth perception. Unfortunately, the Visualization Toolkit does not offer these features, and so in this paper a modified vtkGPUVolumeRayCastMapper is presented. This modified version allows volumetric isosurface rendering as well as receiving shadows from polygons using the usual pipeline.
Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes
Authors: Mosaliganti Kishore , Smith Benjamin , Gelas Arnaud , Gouaillard Alexandre , Megason Sean
Published: January 2022

An Insight Toolkit (ITK) processing framework for segmenting and tracking nuclei in time-lapse microscopy images using coupled active contours is presented in this paper. We implement the method of Dufour et al.[2] to segment and track cells in fluorescence microscopy images. The basic idea is to model the image as a constant intensity background with constant intensity foreground components. We utilizes our earlier submissions on the Chan and Vese algorithm [1] and its multiphase extension [5] to build our new tracking filter. The tracking filter itk::MultiphaseLevelSetTracking inputs a segmentation result (or a coarse estimate) from the previous time-point along with the feature image and generates a new segmentation output. By iteratively repeating this process across all time-points, real-time tracking is made possible. We include 2D/3D example code, parameter settings and show the results generated on a 2D zebrafish embryo image series.
Implementation of a 3D thinning algorithm
Authors: Homann Hanno
Published: January 2022

ITK currently comes with a 2D binary thinning (skeletonisation) method, but does not support 3D or higher. This paper documents a new itkBinaryThinningImageFilter3D and recommends to rename the current filter as itkBinaryThinningImageFilter2D.

The 3D method suggested here is a direct implementation of the work of Lee et al. [2] who have demonstrated that their algorithm can find all deletable surface points at every iteration and is thus very fast. The code was tested on six clinical datasets.
The Use of Robust Local Hausdorff Distances in Accuracy Assessment for Image Alignment of Brain MRI
Authors: Billet Eric , Fedorov Andriy , Chrisochoides Nikos
Published: January 2022

We present and implement an error estimation protocol in the Insight Toolkit (ITK) for assessing the accuracy of image alignment. We base this error estimation on a robust version of the HausdorffDistance (HD) metric applied to the recovered edges of the images. The robust modifications we introduce to the HD metric significantly reduce the amount of outliers in the local distance error estimation. We evaluate the accuracy of our protocol on synthetically deformed images. We provide the source code and datasets to reproduce this evaluation. The proposed method is shown to improve error assessment when it is compared with conventional HD methods. This approach has many applications including local estimation and visual assessment of registration error and registration parameter selection.
An Open Source, Fast Ultrasound B-Mode Implementation for Commodity Hardware
Authors: Mccormick Matthew
Published: January 2022

This document describes an open source, high performance ultrasound B-Mode implementation based on the Insight Toolkit (ITK). ITK extensions are presented to calculate the radio-frequency (RF) signal envelope. A variety of 1D Fast Fourier Transform options are introduced including VNL, FFTW, and an OpenCL solution. Scan conversion is implemented for phased array or curvilinear transducers. The entire image processing pipeline is streamable to limit memory consumption during multi-frame or 3D acquisitions with the introduction of an itk::StreamingResampleImageFilter.
Combining Transforms in ITK
Authors: Klein Stefan , Staring Marius
Published: January 2022

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 , which implements what we call an . Two ways to combine transforms are implemented, by addition and by composition. Depending on this selection, different implementations of the are provided. Also the expressions for the Jacobian and the inverse transform depend on the way transforms are combined. By using function pointers expensive -statements are avoided. This paper is accompanied with the source code.
A VTK-based, CUDA-optimized Non-Parametric Vessel Detection Method
Authors: Alpoge Levent , Joshi Alark , Scheinost Dustin , Onofrey John , Qian Xiaoning , Papademetris Xenophon
Published: January 2022

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 capabilities in commodity graphics hardware using Compute Unified Device Architecture (CUDA). We present the results of our performance analysis and provide source code and examples to validate the reproducibility of our results.
Variance Image Filter
Authors: Tamburo Robert
Published: January 2022

This paper describes an intensity image filter for computing the variance of pixel values contained within a neighborhood centered at each input pixel. The output image contains the calculated variance at each input pixel location. Variance calculations can be restricted by setting an image mask. This paper is accompanied with source code for the filter and test, test images and parameters, and expected output images.
Loopy Belief Propagation on MRFs in ITK
Authors: Doria David
Published: January 2022

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 tutorial on loopy belief propagation on MRFs is available here:

https://github.com/daviddoria/Tutorials/blob/master/BeliefPropagation/BeliefPropagation.pdf?raw=true

The code at the time of this submission is here: https://github.com/daviddoria/BinaryDenoising/commit/e8bd152723584c3af7e30b5e529b8a80f2f2ee5c

And the latest version will be here: https://github.com/daviddoria/BinaryDenoising
Higher Order Accurate Derivative and Gradient Calculation in ITK
Authors: Mccormick Matthew
Published: January 2022

In this article we describe higher order accurate derivative and gradient image ﬁlters for the InsightToolkit. These filters are central difference-based numerical derivative approximations that account for additional Taylor series terms and are based on the expressions given by Khan and Ohba.
Analisis Kemandirian Belajar Matematika dan Peran Keluarga selama Pembelajaran di Era New Normal
Authors: Triana Lisa , Wibowo Sarwo Edy , Putriawati Wiwin
Published: January 2022

Tujuan dari penelitian ini adalah untuk menganalisis kemandirian belajar Matematika dan peran keluarga selama pembelajaran di era new normal. Jenis penelitian yang digunakan adalah penelitian deskriptif kuantitatif dengan menggunakan 12 subjek penelitian. Teknik pengumpulan data yang digunakan dokumentasi dan angket. Hasil pada penelitian ini adalah kemandirian siswa MTS NW Harapan Jaya Orong Telu menunjukkan 34% siswa belum mandiri dalam belajar dan 66% siswa telah mampu belajar mandiri selama new normal. 50% orang tua siswa berperan aktif dalam mengajar kemandirian anak dan 50% berperan secara pasif. Hasil uji korelasi menunjukkan ada hubungan kemandirian siswa MTS NW Harapan Jaya Orong Telu dengan peran orang tuanya dalam mengajar mereka.
Penerapan Metode Pembelajaran Kooperatif Tipe Team Accelerated Instruction (TAI) untuk Meningkatkan Aktivitas dan Prestasi Belajar Bahasa Inggris di Kelas XI IPA 4 SMA Negeri 3 Dompu Tahun Pembelajaran 2019/2020
Authors: Akmal Akmal
Published: January 2022

Penelitian ini bertujuan untuk mengetahui dampak penerapan metode kooperatif tipe TAI yang dikenakan pada siswa kelas XI IPA 4 SMA Negeri 3 Dompu Semester Ganjil tahun pelajaran 2019/2020 terhadap: 1) aktivitas siswa dalam proses pembelajaran Bahasa Inggris, 2) prestasi belajar Bahasa Inggris dan 3) tanggapan siswa terhadap penerapan metode kooperatif tipe TAI. Untuk mencapai tujuan tersebut, diimplementasikan metode kooperatif tipe TAI terhadap siswa kelas XI IPA 4 SMA Negeri 3 Dompu Semester Ganjil tahun pelajaran 2018/2019 yang terdiri atas 32 orang. Data dikumpulkan menggunakan 1) lembar observasi, 2) tes prestasi belajar dan 3) angket. Selanjutnya data yang terkumpul dalam penelitian ini dianalisis secara deskriptif. Hasil penelitian ini menunjukkan bahwa 1) terjadi peningkatan aktivitas belajar siswa yaitu pada siklus I sebesar 11,16 (cukup aktif) dan pada siklus II mencapai 16,38 (aktif), 2) terjadi peningkatan prestasi belajar siswa yaitu pada siklus I dengan nilai rata-rata kelas sebesar 67,88 dan pada siklus II menjadi 74,69, daya serap meningkat dari siklus I sebesar 67,88% menjadi 74,69% pada siklus II dan persentase ketuntasan  meningkat dari siklus I sebesar 81,25% menjadi 90,63% pada siklus II dan 3) tanggapan siswa terhadap metode pembelajaran kooperatif tipe STAD sebesar 38,78 tergolong positif.
Perspektif Lokalitas Bahan Pangan Alternatif bagi Masyarakat: Studi Eksperimental Pemberian Cucur Beras Merah terhadap Penderita Diabetes Melitus Tipe 2
Authors: Fathurrahman Teguh , Imanuddin Imanuddin , Atoy Lena , Jelina Astri
Published: January 2022

Jenis penelitian ini adalah penelitian eksperimental dengan desain penelitian pre and post control desain. Pada penelitian ini akan melihat efektifitas pemberian kue cucur tepung beras merah dalam menurunkan kadar glukosa darah penderita Diabetes Melitus di wilayah kerja puskesmas Kulisusu kabupaten buton utara. Populasi dalam penelitian ini sebanyak 113 pasien rawat jalan di wilayah kerja Puskesmas Kulisusu. Sedangkan sampel dalam penelitian ini sebanyak 30. Analisis yang digunakan dalam penelitian ini terdiri dari analisis univariat dan analisis bivariat menggunakan uji statistik T Test, Hasil analisa menggunakan uji statistik Paired T Test diperoleh nilai t hitung 22,027 > t tabel 2,045 yang menunjukkan terdapat pengaruh pemberian kue cucur tepung beras merah terhadap kadar glukosa darah puasa penderita Diabetes Mellitus tipe 2 di wilayah kerja Puskesmas Kulisusu Kabupaten Buton Utara. Pemberian cucur beras merah ini mampu menekan laju kadar glukosa darah sebesar 42,4% pada kelompok perlakuan yang dilihat pada persen selisih rata-rata kadar glukosa darah puasa dan glukosa darah 2 jam PP, Terdapat pengaruh pemberian cucur beras merah terhadap kadar glukosa darah penderita diabetes mellitus tipe 2 di wilayah kerja Puskesmas Kulisusu Kabupaten Buton Utara ketika dilihat hasil analisis statistik nilai t hitung 22,027 > t tabel 2,045, yang mana produk tersebut mampu menekan laju kadar glukosa darah 2 jam PP sebesar 42,4% pada kelompok perlakuan. Produk cucur beras merah juga disukai oleh para panelis yang mana panelis tersebut merupakan penderita Diabetes Mellitus Tipe 2 di wilayah kerja Puskesmas Kulisusu Kabupaten Buton Utara setelah dilihat dari beberapa aspek penilaian seperti warna, aroma, rasa dan tekstur.
Tukad Bindu Yang Windu: Upaya Mengembalikan Kejayaannya sebagai Urban Tourist Attraction di Denpasar
Authors: Lestari Ayu Putu Utari Parthami , Suwastawa I Putu Agus
Published: January 2022

Sungai sudah sejak lama merupakan lokasi yang penting bagi kehidupan masyarakat, namun di sisi lain, sungai-sungai terdesak oleh pembangunan hingga bahkan menjadi tempat pembuangan limbah baik rumah tangga dan industri. Padahal sungai memiliki potensi untuk dikembangkan menjadi daya tarik wisata yang bermanfaat tidak hanya untuk lingkungan, namun juga bahkan secara ekonomi bagi masyarakat sekitar. Seperti Tukad Bindu, sebuah sungai di Denpasar yang menjadi pilot project pertama pengelolaan daerah aliran sungai yang berbasis komunitas. Yayasan Tukad Bindu sebagai mitra pengabdian menghadapi masalah akibat ditutupnya kawasan dalam upaya memutus mata rantai penyebaran Covid-19, seperti penurunan kualitas fisik hingga kekhawatiran akan kunjungan wisatawan yang tidak setinggi dulu ketika lokasi nanti dibuka kembali. Solusi yang ditawarkan oleh tim pengabdian masyarakat Universitas Ngurah Rai di Tukad Bindu antara lain pelaksanaan desain backdrop panggung, atap salah satu fasilitas, papan penunjuk, pelaksanaan sosialisasi eco enzyme dan lomba mewarnai. Seluruh kegiatan dilakukan bersama-sama dengan masyarakat difasilitasi oleh yayasan, sejak perencanaan, pelaksanaan hingga pemantauan. Seluruh kegiatan mendapatkan dukungan dan apresiasi dari semua pihak yang ditandai dengan keberhasilan pelaksanaan kegiatan sesuai target.
Hubungan Pola Asuh Orangtua dengan Persepsi Pencapaian Perkembangan Kognitif Anak SD di Masa Pembelajaran Jarak Jauh
Authors: Ony Nathania Immanuela , Handayani Penny
Published: January 2022

Pendidikan adalah salah satu hal yang penting bagi perkembangan anak sekolah dasar (SD). Pada umumnya, proses pembelajaran di sekolah dilakukan secara tatap muka di dalam kelas (pembelajaran langsung). COVID-19 muncul dengan cara penyebaran yang mudah dan membuat pemerintah mengeluarkan kebijakan Belajar Dari Rumah. Hal ini menguatkan kembali peran orangtua sebagai pendidik utama anak, yang diterapkan dengan pola pengasuhan yang berbeda-beda. Oleh karena itu, penelitian ini bertujuan untuk menjelaskan hubungan antara pola asuh orangtua dengan persepsi pencapaian perkembangan kognitif anak SD pada masa Pembelajaran Jarak Jauh. Sebanyak 220 partisipan telah mengisi kuesioner melalui google forms dan dianalisis dengan metode Spearman Correlation. Hasil penelitian ini menunjukkan korelasi yang signifikan antara kedua variabel (r(218) = 0.343, p<.01), yang menandakan adanya hubungan antara pola asuh orangtua dengan persepsi pencapaian perkembangan kognitif anak SD pada masa Pembelajaran Jarak Jauh.
Investigation of Structures of Sintered Processed Fly Ash Materials: Resources of Industrial Wastes
Authors:   PG Department Materials Science, Maharaja Sriram Chandra Bhanja Deo University, Keonjhar Campus, Odisha, India, M.K Panigrahi
Published: January 2022

The aim of the work is to use industrial waste as resource materials for formulating useful product for society. Materials are prepared using Fly ash as main ingredient through sintered process via solid state route. Different materials are prepared using various sintering temperature. The crystal structural and phases are explored by XRD analysis. Mulite phase are investigated, which is indicated the insulating properties of the materials. Surface topography of the prepared materials is analyzed by FESEM characterization. EDS analysis is also done during the FESEM characterization and is assessed the various chemical compositions. Identification of different chemical groups in the processed Fly Ash is carried out by FTIR analysis. Highest electrical resistivity is estimated and is found to be 35.1 MΩ, which indicates the very good insulating property.