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Surface Mesh Discrete Curvature Estimators
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Computing local curvatures of a given surface is important for applications, shape analysis, surface segmentation, meshing, and surface evolution. For a given smooth surface (with a given analytical expression which is sufficiently differentiable) curvatures [...]

Surface Mesh Normals Filter
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We have previously developed a new surface mesh data structure in itk (code{itk::QuadEdgeMesh}~cite{itkQE}). In this document we describe a new filter (code{itk::QENormalFilter}) to estimate normals for a given triangular surface mesh in this data structure. [...]

Surface Meshes Smoothing
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This paper describes the implementation of a surface smoothing filter in ITK, based ont he Quad Edge Mesh surface data structure.

An Adaptive Thresholding Image Filter
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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 [...]

Support for Streaming the JPEG2000 File Format
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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 [...]

Surface Meshes Incremental Decimation Framework
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When dealing with meshes, it is often preferable to work with a lower resolution mesh for computational time purpose, display. The process of reducing a given mesh, mesh decimation, is thus an important step in most of pipeline dealing with meshes. [...]

Mutable Priority Queue Container
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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 [...]

Triangular Meshes Delaunay Conforming Filter
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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 [...]

Microscopy Image Analysis: Blob Segmentation using Geodesic Active Contours
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An Insight Toolkit (ITK) processing framework for blob segmentation with applications to microscopy images is presented in this paper. Our algorithm is a reļ¬nement of the work of Mosaliganti et al. [3] for splitting cell clusters. The basic idea is to [...]

An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects
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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 [...]

level set segmentation using coupled active surfaces
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An Insight Toolkit (ITK) processing framework for simultaneous segmentation of multiple objects using active contours without edges is presented in this paper. These techniques are also popularly referred to as multiphase methods. Earlier, we had an [...]

Cell Tracking using Coupled Active Surfaces for Nuclei and Membranes
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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 [...]

CTest Integration of Sikuli Automated GUI Testing
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In order to test our software GoFigure2 for the visualization and the processing of extremely large 3D+t microscopy images, we utilized the visual programming technology Sikuli to automate our GUI testing. We then integrated these Sikuli tests into CTest [...]

Level Set Segmentation: Active Contours without edge
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An Insight Toolkit (ITK) processing framework for segmentation using active contours without edges is presented in this paper. Our algorithm is based on the work of Chan and Vese [1] that uses level- sets to accomplish region segmentation in images with [...]

A simple Qt based comparison program for ITK and VTK images.
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This document describes a project that can compare many images simultaneously in a synchronized manner. Such an application can be used in any ITK/VTK image processing pipelines; the programmer can use it to quickly visualize and compare intermediate results [...]

GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to system biolgy
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As part of the Center of Excellence in Genomic Science at Caltech, we have initiated the Digital Fish Project. Our goal is to use in toto imaging of developing transgenic zebrafish embryos on a genomic scale to acquire digital, quantitative, cell-based, [...]


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