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Parameterization of discrete surfaces
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Parameterization of surfaces, sometimes alled ”‘flattening”’ as it maps a surface embedded in 3D into its intrinsic 2D domain, is a powerfull tool for the analysis of surfaces. For the past years, there has been a growing interest in the Community [...]

Incremental Delaunay Triangulation
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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 [...]

Walk In A Triangulation : Straight Walk
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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 [...]

Exact Geometrical Predicate: Point in circle
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This document describes the implementation in ITK of the "point in circle" geometrical predicate. Based on Jonathan Shewchuk's work which implements an exact version of the predicate using standard floating point types and arithmetic, the implementation [...]

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.

Primal/Dual Mesh with Application to Triangular/Simplex Mesh and Delaunay/Voronoi
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This document describes an extension of ITK to handle both primal and dual meshes simultaneously. This paper describe in particular the data structure, an extension of itk::QuadEdgeMesh, a filter to compute and add to the the structure the dual of an existing [...]

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 [...]

ItkQuadEdgeMesh: A Discrete Orientable 2-Manifold Data Structure for Image Processing
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There is nowadays an increasing need in interaction between discrete surfaces (2-manifolds) and images. More specifically, segmentation and registration of n-dimensional images are taking advantage of a priori geometrical information, most often provided as [...]

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 refinement of the work of Mosaliganti et al. [3] for splitting cell clusters. The basic idea is to [...]

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 [...]

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 [...]

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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