3D Geometric Analysis of Tubular Objects based on Surface Normal Accumulation

This paper proposes a simple and efficient method for the reconstruction and extraction of geometric parameters from 3D tubular objects. Our method constructs an image that accumulates surface normal information, then peaks within this image are located by tracking. Finally, the positions of these are optimized to lie precisely on the tubular shape centerline. This method is very versatile, and is able to process various input data types like full or partial mesh acquired from 3D laser scans, 3D height map or discrete volumetric images. The proposed algorithm is simple to implement, contains few parameters and can be computed in linear time with respect to the number of surface faces. Since the extracted tube centerline is accurate, we are able to decompose the tube into rectilinear parts and torus-like parts. This is done with a new linear time 3D torus detection algorithm, which follows the same principle of a previous work on 2D arc circle recognition. Detailed experiments show the versatility, accuracy and robustness of our new method.Comment: in 18th International Conference on Image Analysis and Processing, Sep 2015, Genova, Italy. 201

Ellipse-based Principal Component Analysis for Self-intersecting Curve Reconstruction from Noisy Point Sets

Surface reconstruction from cross cuts usually requires curve reconstruction from planar noisy point samples -- The output curves must form a possibly disconnected 1manifold for the surface reconstruction to proceed -- This article describes an implemented algorithm for the reconstruction of planar curves (1manifolds) out of noisy point samples of a sel-fintersecting or nearly sel-fintersecting planar curve C -- C:[a,b]⊂R→R is self-intersecting if C(u)=C(v), u≠v, u,v∈(a,b) (C(u) is the self-intersection point) -- We consider only transversal self-intersections, i.e. those for which the tangents of the intersecting branches at the intersection point do not coincide (C′(u)≠C′(v)) -- In the presence of noise, curves which self-intersect cannot be distinguished from curves which nearly sel fintersect -- Existing algorithms for curve reconstruction out of either noisy point samples or pixel data, do not produce a (possibly disconnected) Piecewise Linear 1manifold approaching the whole point sample -- The algorithm implemented in this work uses Principal Component Analysis (PCA) with elliptic support regions near the selfintersections -- The algorithm was successful in recovering contours out of noisy slice samples of a surface, for the Hand, Pelvis and Skull data sets -- As a test for the correctness of the obtained curves in the slice levels, they were input into an algorithm of surface reconstruction, leading to a reconstructed surface which reproduces the topological and geometrical properties of the original object -- The algorithm robustly reacts not only to statistical noncorrelation at the self-intersections(nonmanifold neighborhoods) but also to occasional high noise at the nonselfintersecting (1manifold) neighborhood

Extracting curve-skeletons from digital shapes using occluding contours

Curve-skeletons are compact and semantically relevant shape descriptors, able to summarize both topology and pose of a wide range of digital objects. Most of the state-of-the-art algorithms for their computation rely on the type of geometric primitives used and sampling frequency. In this paper we introduce a formally sound and intuitive definition of curve-skeleton, then we propose a novel method for skeleton extraction that rely on the visual appearance of the shapes. To achieve this result we inspect the properties of occluding contours, showing how information about the symmetry axes of a 3D shape can be inferred by a small set of its planar projections. The proposed method is fast, insensitive to noise, capable of working with different shape representations, resolution insensitive and easy to implement

Total Denoising: Unsupervised Learning of 3D Point Cloud Cleaning

We show that denoising of 3D point clouds can be learned unsupervised, directly from noisy 3D point cloud data only. This is achieved by extending recent ideas from learning of unsupervised image denoisers to unstructured 3D point clouds. Unsupervised image denoisers operate under the assumption that a noisy pixel observation is a random realization of a distribution around a clean pixel value, which allows appropriate learning on this distribution to eventually converge to the correct value. Regrettably, this assumption is not valid for unstructured points: 3D point clouds are subject to total noise, i. e., deviations in all coordinates, with no reliable pixel grid. Thus, an observation can be the realization of an entire manifold of clean 3D points, which makes a na\"ive extension of unsupervised image denoisers to 3D point clouds impractical. Overcoming this, we introduce a spatial prior term, that steers converges to the unique closest out of the many possible modes on a manifold. Our results demonstrate unsupervised denoising performance similar to that of supervised learning with clean data when given enough training examples - whereby we do not need any pairs of noisy and clean training data.Comment: Proceedings of ICCV 201

Flexural Rigidity Measurements of Biopolymers Using Gliding Assays

Microtubules are cytoskeletal polymers which play a role in cell division, cell mechanics, and intracellular transport. Each of these functions requires microtubules that are stiff and straight enough to span a significant fraction of the cell diameter. As a result, the microtubule persistence length, a measure of stiffness, has been actively studied for the past two decades. Nonetheless, open questions remain: short microtubules are 10-50 times less stiff than long microtubules, and even long microtubules have measured persistence lengths which vary by an order of magnitude. Here, we present a method to measure microtubule persistence length. The method is based on a kinesin-driven microtubule gliding assay. By combining sparse fluorescent labeling of individual microtubules with single particle tracking of individual fluorophores attached to the microtubule, the gliding trajectories of single microtubules are tracked with nanometer-level precision. The persistence length of the trajectories is the same as the persistence length of the microtubule under the conditions used. An automated tracking routine is used to create microtubule trajectories from fluorophores attached to individual microtubules, and the persistence length of this trajectory is calculated using routines written in IDL. This technique is rapidly implementable, and capable of measuring the persistence length of 100 microtubules in one day of experimentation. The method can be extended to measure persistence length under a variety of conditions, including persistence length as a function of length along microtubules. Moreover, the analysis routines used can be extended to myosin-based acting gliding assays, to measure the persistence length of actin filaments as well