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The computation speed for distance transforms becomes important in a wide variety of image processing applications. Current ITK library filters do not see any benefit from a multithreading environment. We introduce a three-dimensional signed parallel [...]
VoxBo (www.voxbo.org) is a distributed processing framework, developed at the Center of Functional Neuroimaging at the University of Penssylvania, with the purpose of processing and analyzing brain functional MRI data.
VoxBo is written in C++, and it is [...]
The deconvolution, also called deblurring, tries to revert the optical distortion introduced during the aquisition of the image. It is a family of image processing which can be classed in the larger family of image restoration.
Deconvolution is a very [...]
A Generalized Squared Euclidean Distance Transform with Voronoi Maps
Published in The Insight Journal
Published in The Insight Journal
This document describes the implementation of an algorithm that computes a generalization of the distance transform with the squared euclidean metric.
The generalization allows for interesting image operators, e.g. a morphologic dilation with euclidean ball [...]
Integration of the Java Image Science Toolkit with E-Science Platform
Published in The Insight Journal
Published in The Insight Journal
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 [...]
A MultipleImageIterator for iterating over multiple images simultaneously
Published in The Insight Journal
Published in The Insight Journal
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. [...]
Open Source Software to Visualize Complex Data on Remote CEA's Supercomputing Facilities
Published in The MIDAS Journal
Published in The MIDAS Journal
In order to guaranty performances of complex systems using numerical simulation, CEA is performing advanced data analysis and scientific visualization with open source software using High Performance Computing (HPC) capability. The diversity of the physics to [...]
This talk presents the Open-Source toolkits developed by Kitware for big data analysis.
Deformable Registration with Discontinuity Preservation using Multi-Scale MRF
Published in The MIDAS Journal
Published in The MIDAS Journal
Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate [...]
This document describes the implementation of a simple command line argument parser using the Insight Toolkit ITK. Such a parser may be useful for use in the examples of the ITK. This paper is accompanied with the source code.
Next Generation of the JAVA Image Science Toolkit (JIST) Visualization and Validation
Published in The Insight Journal
Published in The Insight Journal
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 [...]
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 [...]
This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an [...]
Small Computings for Clinicals and SCCToolKit, OR friendly Trial Package and Software Development Kit
Published in The MIDAS Journal
Published in The MIDAS Journal
This paper is about a design policy for operation-room (OR) friendly research system, software and a software toolkit SCCToolKit for this purpose, and a few examples. Examples are image processor for endoscope, OR event detector, vision based registration of [...]
The Insight Segmentation and Registration Toolkit (ITK) previously provided a framework for parsing Extensible Markup Language (XML) documents using the Simple API for XML (SAX) framework. While this programming model is memory efficient, it places most of [...]
A Streaming IO Base Class and Support for Streaming the MRC and VTK File Format
Published in The Insight Journal
Published in The Insight Journal
This paper describes our contribution of three new classes to the Insight Toolkit community. We present a new ImageIO base class for streaming image file, along with two derived ImageIO classes for the VTK and the MRC file formats.
The Insight Segmentation and Registration Toolkit (www.itk.org) has become a standard in academia and industry for medical image analysis. In recent years, the ITK developers' community has focused on providing programming interfaces to ITK from Python, Java, [...]
When an image is mostly composed of background pixels, most of the automatic
thresholding methods are failing to produce a relevant threshold. This is mainly
caused because one mode is over represented compared to the other in the histogram
of the image. [...]
We have recently detailed the procedure for building ITK on the iOS. In this work, we contribute itkiOSImageIO , the necessary ITK class that provides the input/output (IO) interface with the repository of images stored on iOS Apple devices, such as the iPod [...]
MUSiiC ToolKit 2.0: Bidirectional Real-time Software Framework for Advanced Interventional Ultrasound Research
Published in The MIDAS Journal
Published in The MIDAS Journal
Ultrasound (US) imaging is a popular and convenient medical imaging modality thanks to its mobility, non-ionizing radiation, ease-of-use, and real-time acquisition. Conventional US imaging is frequently integrated with tracking systems and robotic systems in [...]
When dealing with functional minimization, or maximization, it can sometimes be solved by a greedy algorithm. To implement greedy algorithm one needs priority queue container, i.e. get for a very low cost the lowest or highest element present in a sorted [...]
ITK's flood filling iterator represents a way to visit pixels/voxels within an image having a specific connectivity. The iterator is initialized at known seed points and starting from these, neighbors that are within the desired connectivity are marked as to [...]
The emph{Delaunay triangulation} 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, emph{Delaunay [...]
This document describes a module for the Insight Toolkit (ITK) to assist in performance
benchmarking and a suite of benchmarks for the toolkit. These resources provide metrics to quantify
software computational performance. This is a pre-requisite to improve [...]
At the Johns Hopkins University’s Engineering Research Center for Computer-Integrated Surgical Systems and Technology (ERC-CISST) laboratory, we have designed and developed a platformindependent C++ software package, called the nArray library, that provides [...]
Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy
Published in The Insight Journal
Published in The Insight Journal
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 [...]
An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects
Published in The Insight Journal
Published in The Insight Journal
An Insight Toolkit (ITK) algorithm for detection of spherical objects using Hough methods with voting is presented in this paper. Currently, the usage of Hough methods for detecting linear and circular elements exists for 2D images in ITK. The current work [...]
In this work,
we extend a previously demonstrated entropy based groupwise registration method
to include a non-rigid deformation model based on B-splines.
We describe an open source implementation of the groupwise registration algorithm
using the [...]
ly in ITK, the only way to find the contour of the objects in a binary image is to use the BinaryErodeImageFilter, with a kernel of radius 1. This filter is a generic filter, made to support any shape and size of structuring element, and thus is not optimized [...]
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 [...]
Radial Thickness Calculation and Visualization for Volumetric Layers
Published in The Insight Journal
Published in The Insight Journal
Volumetric layers often encountered in medical image analysis are characterized by double and nested bounding surfaces. The thickness of a volumetric layer at a point on the bounding surface is the distance from that point to the opposite surface. There exist [...]
An Open Source, Fast Ultrasound B-Mode Implementation for Commodity Hardware
Published in The Insight Journal
Published in The Insight Journal
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 [...]
Richard Beare has recently introduced a new filter to efficiently labelize the connected components with ITK, and has also proposed to use the run-length encoding used in that filter to implement some of the most useful binary mathematical morphology [...]
An entropy based multi-thresholding method for semi-automatic segmentation of liver tumors
Published in The MIDAS Journal
Published in The MIDAS Journal
Liver cancer is the fifth most commonly diagnosed cancer and the third most common cause of death
from cancer worldwide. A precise analysis of the lesions would help in the staging of the tumor and
in the evaluation of the possible applicable therapies. In [...]
