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.

Multi-scale Steerable Phase-Symmetry Filters for ITK

Thresholding is perhaps one of the most basic techniques in image processing. The Insight Toolkit (ITK) includes several threshold filters ranging from simple ones to Otsu based thresholding. Deep into the implementation of the Canny edge detection filter, ITK includes an implementation of hysteresis thresholding, but unfortunately this method can not be used as a generic filter.
This paper presents an implementation of the hysteresis thresholding filter that can be used as a standalone ITK filter.

A Threshold with Hysteresis

This document describes the implementation using the Insight Toolkit of an algorithm for detecting creases (ridges and valleys) in N-dimensional images, based on the Local Structure Tensor of the image. In addition to the filter used to calculate the creaseness image, a filter for the computation of the structure tensor is also included in this submission.

Multilocal Creaseness Measure

The recent ITKv4 refactoring includes several enhancements to the existing registration framework. These additional transform classes provide access to mappings described by dense displacement fields and their corresponding optimization which complement the popular free-form deformation (FFD) ap- proach already in ITK. Innovation motivated by previous work [5] and recent diffeomorphic image regis- tration developments in which the characteristic velocity field is represented by spatiotemporal B-splines [2], resulted in a diffeomorphic B-spline-based image registration algorithm combining and extending these techniques which we make available in ITK through the gerrit system. Additionally, we include two command line tools showcasing the new elements of the registration refactoring for 1) computing mappings between two images (antsRegistration) including the family of transforms discussed in this article and 2) applying those transformations to images (antsApplyTransforms). NB: The user must download the patch available at http://review.source.kitware.com/#/c/3606/ in or- der to compile the code accompanying this article.

The TVDMFFDVR Algorithm

This document describes a contribution to the Insight Toolkit intended to perform landmark-based registration on two meshes. The method implemented here is restricted to meshes with a spherical geometry and topology. Please refer Wahba's paper for the mathematical details and Zou's paper for the applications.
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.

Spherical Thin Plate Spline Mesh Filter

This document describes the implementation in ITK of the Straight Walk in a Triangulation algorithm proposed by Devillers et al. Using the exact discrete geometrical orientation predicate, and the itk::QuadEdgeMesh API of ITK, we propose an efficient implementation that locates a point in a triangulated mesh structure. This paper is accompanied with the source code and examples that should provide enough details for users. This work has for principal intended an exact and robust implementation of a Delaunay triangulation / Voronoi tesselation in ITK, which will be presented in a separate paper, once done.

Walk In A Triangulation : Straight Walk

Unlike the measure of the area in 2D or of the volume in 3D, the perimeter and the surface are not easily measurable in a discretized image.
In this article we describe a method based on the Crofton formula to measure those two parameters in a discritized image. The accuracy of the method is discussed and tested on several known objects. An algorithm based on the run-length encoding of binary objects is presented and compared to other approaches.
An implementation is provided and integrated in the LabelObject/LabelMap framework contributed earlier by the authors.

Efficient N-Dimensional surface estimation using Crofton formula and run-length encoding

The tophat transform is a well know and widely used transform based of morphological opening or closing. It is often used to remove the background in an image, where the background is defined as the zones which do not fit in the user provided kernel.

Similarly, the tophat by area is used to remove the background in an image, but the criteria of selection is the size of the connected component, either in physical size or in number of pixels, and is independent of the shape of the connected component. This property makes the tophat non dependent of the shape of the object and makes easier to describe the criteria.


Tophap by area

This paper documents on-going work to facilitate ITK-based processing and 3D Slicer scene management in ParaView. We believe this will broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView. In this paper, we present KWScene, an open source cross-platform library that is being developed to support implementation of these types of plugins. We describe the overall design of the library and provide implementation details and conclude by presenting a concrete example that demonstrates the use of the KWScene library in computational anatomy research at Johns Hopkins Center for Imaging Science.

Enabling ITK-based processing and 3D Slicer MRML scene management in ParaView

This paper describes the implementation of the LDFFD and TDFFD algorithms. Both quantify motion and deformation from an input image sequence by taking profit of the temporal dimension of velocity fields in the diffeomorphic registration framework to process the input image sequence as a single 3D+t object. The rationale behind these approaches is to formulate motion estimation in an image sequence as a multi-channel registration problem. This paper describes our implementation, currently following the original ITK registration framework without multi-threading and diffeomorphic registration framework.
Migration to ITKv4 will be addressed in future work. We also provide code for computing strain on a segmentation represented as a VTK polydata mesh. Program usages for LDFFD and TDFFD as well as strain quantification results are given for one 3D ultrasound image sequence acquired on a healthy volunteer.