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.

A Simple Command Line Argument Parser

In previous work, we presented an algorithm to synthesize volumetric images of vascular trees and generate the corresponding ground truth segmentations, bifurcation locations, branch properties, and tree hierarchy. In this work, we provide the software needed to simulate these volumes. Our software expects a number of physical parameters and oxygen demand maps to produce 3D volumetric images of vasculature, as well as information about the bifurcation locations, tree hierarchy and branch radii in a GXL file. We foresee our software useful for large scale evaluation studies of medical image segmentation and analysis software.

VascuSynth: Vascular Tree Synthesis Software

This paper describes two 3D micro-CT datasets of 23 and 5.9 Gigabytes that Creatis has made publicly available to the imaging community. These datasets were acquired using Synchrotron Radiation micro-Ct at the ESRF at a spatial resolution of 1.4 microns. The provided datasets were previously included in a study to develop
new 3D imaging methods to analyze, in three-dimensions, the morphology of microcracks
human trabecular bone at the micrometric scale.

This paper is a pure data contribution. The datasets described here are made available in the public MIDAS database. Here we describe the content of the files to make easier for others to use this data as input for their own research work. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.

Acquisition of Synchrotron Radiation micro-CT images for the investigation of bone micro-cracks

We have written a set of classes than enable computation of boolean operations on surface meshes using only VTK classes. In addition to being compatible with the VTK license, our contribution preserves surface mesh topology to the extent possible in boolean operations and passes point data and cell data through to the output mesh where possible.

Boolean Operations on Surfaces in VTK Without External Libraries

This document illustrates how to process large images (5 and 23 Gigabytes in size) by taking advantage of the streaming capabilities of the Insight Toolkit ITK. Here we illustrate two scenarios: (a) the case when the image itself is larger than the computer's RAM, (b) the case when the image is large but still can fit in the computer's RAM. This report is intended to serve as a tutorial on how to take advantage of this memory management capabilities of ITK version 4.

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.

Large Image Streaming using ITKv4

It is often useful to be able to compute the component of image gradient in a direction defined by a shape of some form, rather than relative to the image axis. This article introduces a simple method for doing this based on distance transforms that is potentially useful in a number of applications.


Simple directional gradients

This document describes an extension of the Insight Toolkit (ITK, www.itk.org) for 2D-3D registration with multiple fixed images, that is, registration of a three-dimensional dataset to a group of fixed planar projections. 2D-3D registration is possible with ITK's standard classes but with several limitations: the number of fixed images is restricted to one and the moving image's orientation axes are ignored, which greatly complicates the registration definition. Both problems are solved by the proposed framework, which permits multi-resolution intensity-based registration with an arbitrary number of fixed images, with all images defined in any orientation. In addition, the framework provides implementations of the Normalized Gradient Correlation and Pattern Intensity metrics, which are commonly used in 2D-3D registration but were not present in ITK. This article gives a detailed description of the proposed framework, along with examples that show its capabilities in registrations of real and simulated images of the spine.

An ITK-Based Framework for 2D-3D Registration with Multiple Fixed Images

This papers describes an image filter that counts the number of neighbors a pixel has storing that value at the pixel's image index. Functionality is provided to 1) adjust the neighborhood size, 2) count only those pixels within a specific value range, and 3) only record a neighbor count for specific pixels of interest. This paper is accompanied with source code for the filter and test, test images and parameters, and expected output images.

An Image Filter for Counting Pixel Neighbors

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.


CITK - an architecture and examples of CUDA enabled ITK filters

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.