Minkowski Tensors of Anisotropic Spatial Structure

This article describes the theoretical foundation of and explicit algorithms for a novel approach to morphology and anisotropy analysis of complex spatial structure using tensor-valued Minkowski functionals, the so-called Minkowski tensors. Minkowski tensors are generalisations of the well-known scalar Minkowski functionals and are explicitly sensitive to anisotropic aspects of morphology, relevant for example for elastic moduli or permeability of microstructured materials. Here we derive explicit linear-time algorithms to compute these tensorial measures for three-dimensional shapes. These apply to representations of any object that can be represented by a triangulation of its bounding surface; their application is illustrated for the polyhedral Voronoi cellular complexes of jammed sphere configurations, and for triangulations of a biopolymer fibre network obtained by confocal microscopy. The article further bridges the substantial notational and conceptual gap between the different but equivalent approaches to scalar or tensorial Minkowski functionals in mathematics and in physics, hence making the mathematical measure theoretic method more readily accessible for future application in the physical sciences

Nonparametric joint shape learning for customized shape modeling

We present a shape optimization approach to compute patient-specific models in customized prototyping applications. We design a coupled shape prior to model the transformation between a related pair of surfaces, using a nonparametric joint probability density estimation. The coupled shape prior forces with the help of application-specific data forces and smoothness forces drive a surface deformation towards a desired output surface. We demonstrate the usefulness of the method for generating customized shape models in applications of hearing aid design and pre-operative to intra-operative anatomic surface estimation

The geometry of dynamical triangulations

We discuss the geometry of dynamical triangulations associated with 3-dimensional and 4-dimensional simplicial quantum gravity. We provide analytical expressions for the canonical partition function in both cases, and study its large volume behavior. In the space of the coupling constants of the theory, we characterize the infinite volume line and the associated critical points. The results of this analysis are found to be in excellent agreement with the MonteCarlo simulations of simplicial quantum gravity. In particular, we provide an analytical proof that simply-connected dynamically triangulated 4-manifolds undergo a higher order phase transition at a value of the inverse gravitational coupling given by 1.387, and that the nature of this transition can be concealed by a bystable behavior. A similar analysis in the 3-dimensional case characterizes a value of the critical coupling (3.845) at which hysteresis effects are present.Comment: 166 pages, Revtex (latex) fil

Measuring the Geometry and Topology of Large Scale Structure using SURFGEN: Methodology and Preliminary Results

We present a new ansatz which can successfully be used to determine the morphological properties of the supercluster-void network. The ansatz is based on a surface modelling scheme SURFGEN, which generates a triangulated surface from a discrete data set representing (say) the distribution of galaxies in real (or redshift) space. Four Minkowski functionals -- surface area, volume, extrinsic curvature and genus -- describe the geometry and topology of the supercluster-void network. Ratio's of Minkowski functionals -- Shapefinders -- provide us with an excellent diagnostic of three dimensional shapes of clusters, superclusters and voids. Minkowski functionals and Shapefinders are determined for a triangulated iso-density surface using SURFGEN. SURFGEN is tested against both simply and multiply connected eikonal surfaces such as triaxial ellipsoids and tori. Remarkably, the first three Minkowski functionals are computed to better than 1% accuracy while the fourth (genus) is known exactly. SURFGEN also gives excellent results when applied to Gaussian random fields. Our results indicate that the surface modelling scheme SURFGEN is accurate and robust and can successfully be used to quantify the topology and morphology of the supercluster-void network in the universe. We apply SURFGEN to three cosmological models, \LCDM, \TCDM and SCDM and obtain interesting new results pertaining to the geometry, morphology and topology of large scale structure.Comment: 28 MNRAS-style pages, 24 figures -- Revised with enhanced discussion and added references. An appendix included which shows that SURFGEN gives excellent results when applied to Gaussian Random Fields. Accepted for publication in MNRA

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Subdivision Shell Elements with Anisotropic Growth

A thin shell finite element approach based on Loop's subdivision surfaces is proposed, capable of dealing with large deformations and anisotropic growth. To this end, the Kirchhoff-Love theory of thin shells is derived and extended to allow for arbitrary in-plane growth. The simplicity and computational efficiency of the subdivision thin shell elements is outstanding, which is demonstrated on a few standard loading benchmarks. With this powerful tool at hand, we demonstrate the broad range of possible applications by numerical solution of several growth scenarios, ranging from the uniform growth of a sphere, to boundary instabilities induced by large anisotropic growth. Finally, it is shown that the problem of a slowly and uniformly growing sheet confined in a fixed hollow sphere is equivalent to the inverse process where a sheet of fixed size is slowly crumpled in a shrinking hollow sphere in the frictionless, quasi-static, elastic limit.Comment: 20 pages, 12 figures, 1 tabl

Geometric data understanding : deriving case specific features

There exists a tradition using precise geometric modeling, where uncertainties in data can be considered noise. Another tradition relies on statistical nature of vast quantity of data, where geometric regularity is intrinsic to data and statistical models usually grasp this level only indirectly. This work focuses on point cloud data of natural resources and the silhouette recognition from video input as two real world examples of problems having geometric content which is intangible at the raw data presentation. This content could be discovered and modeled to some degree by such machine learning (ML) approaches like deep learning, but either a direct coverage of geometry in samples or addition of special geometry invariant layer is necessary. Geometric content is central when there is a need for direct observations of spatial variables, or one needs to gain a mapping to a geometrically consistent data representation, where e.g. outliers or noise can be easily discerned. In this thesis we consider transformation of original input data to a geometric feature space in two example problems. The first example is curvature of surfaces, which has met renewed interest since the introduction of ubiquitous point cloud data and the maturation of the discrete differential geometry. Curvature spectra can characterize a spatial sample rather well, and provide useful features for ML purposes. The second example involves projective methods used to video stereo-signal analysis in swimming analytics. The aim is to find meaningful local geometric representations for feature generation, which also facilitate additional analysis based on geometric understanding of the model. The features are associated directly to some geometric quantity, and this makes it easier to express the geometric constraints in a natural way, as shown in the thesis. Also, the visualization and further feature generation is much easier. Third, the approach provides sound baseline methods to more traditional ML approaches, e.g. neural network methods. Fourth, most of the ML methods can utilize the geometric features presented in this work as additional features.Geometriassa käytetään perinteisesti tarkkoja malleja, jolloin datassa esiintyvät epätarkkuudet edustavat melua. Toisessa perinteessä nojataan suuren datamäärän tilastolliseen luonteeseen, jolloin geometrinen säännönmukaisuus on datan sisäsyntyinen ominaisuus, joka hahmotetaan tilastollisilla malleilla ainoastaan epäsuorasti. Tämä työ keskittyy kahteen esimerkkiin: luonnonvaroja kuvaaviin pistepilviin ja videohahmontunnistukseen. Nämä ovat todellisia ongelmia, joissa geometrinen sisältö on tavoittamattomissa raakadatan tasolla. Tämä sisältö voitaisiin jossain määrin löytää ja mallintaa koneoppimisen keinoin, esim. syväoppimisen avulla, mutta joko geometria pitää kattaa suoraan näytteistämällä tai tarvitaan neuronien lisäkerros geometrisia invariansseja varten. Geometrinen sisältö on keskeinen, kun tarvitaan suoraa avaruudellisten suureiden havainnointia, tai kun tarvitaan kuvaus geometrisesti yhtenäiseen dataesitykseen, jossa poikkeavat näytteet tai melu voidaan helposti erottaa. Tässä työssä tarkastellaan datan muuntamista geometriseen piirreavaruuteen kahden esimerkkiohjelman suhteen. Ensimmäinen esimerkki on pintakaarevuus, joka on uudelleen virinneen kiinnostuksen kohde kaikkialle saatavissa olevan datan ja diskreetin geometrian kypsymisen takia. Kaarevuusspektrit voivat luonnehtia avaruudellista kohdetta melko hyvin ja tarjota koneoppimisessa hyödyllisiä piirteitä. Toinen esimerkki koskee projektiivisia menetelmiä käytettäessä stereovideosignaalia uinnin analytiikkaan. Tavoite on löytää merkityksellisiä paikallisen geometrian esityksiä, jotka samalla mahdollistavat muun geometrian ymmärrykseen perustuvan analyysin. Piirteet liittyvät suoraan johonkin geometriseen suureeseen, ja tämä helpottaa luonnollisella tavalla geometristen rajoitteiden käsittelyä, kuten väitöstyössä osoitetaan. Myös visualisointi ja lisäpiirteiden luonti muuttuu helpommaksi. Kolmanneksi, lähestymistapa suo selkeän vertailumenetelmän perinteisemmille koneoppimisen lähestymistavoille, esim. hermoverkkomenetelmille. Neljänneksi, useimmat koneoppimismenetelmät voivat hyödyntää tässä työssä esitettyjä geometrisia piirteitä lisäämällä ne muiden piirteiden joukkoon

Automatic Extraction of Road Points from Airborne LiDAR Based on Bidirectional Skewness Balancing

Road extraction from Light Detection and Ranging (LiDAR) has become a hot topic over recent years. Nevertheless, it is still challenging to perform this task in a fully automatic way. Experiments are often carried out over small datasets with a focus on urban areas and it is unclear how these methods perform in less urbanized sites. Furthermore, some methods require the manual input of critical parameters, such as an intensity threshold. Aiming to address these issues, this paper proposes a method for the automatic extraction of road points suitable for different landscapes. Road points are identified using pipeline filtering based on a set of constraints defined on the intensity, curvature, local density, and area. We focus especially on the intensity constraint, as it is the key factor to distinguish between road and ground points. The optimal intensity threshold is established automatically by an improved version of the skewness balancing algorithm. Evaluation was conducted on ten study sites with different degrees of urbanization. Road points were successfully extracted in all of them with an overall completeness of 93%, a correctness of 83%, and a quality of 78%. These results are competitive with the state-of-the-artThis work has received financial support from the Consellería de Cultura, Educación e Ordenación Universitaria (accreditation 2019-2022 ED431G-2019/04 and reference competitive group 2019-2021, ED431C 2018/19) and the European Regional Development Fund (ERDF), which acknowledges the CiTIUS-Research Center in Intelligent Technologies of the University of Santiago de Compostela as a Research Center of the Galician University System. This work was also supported in part by Babcock International Group PLC (Civil UAVs Initiative Fund of Xunta de Galicia) and the Ministry of Education, Culture and Sport, Government of Spain (Grant Number TIN2016-76373-P)S

Shape measure for identifying perceptually informative parts of 3d objects

We propose a mathematical approach for quantifying shape complexity of 3D surfaces based on perceptual principles of visual saliency. Our curvature variation measure (CVM), as a 3D feature, combines surface curvature and information theory by leveraging bandwidth-optimized kernel density estimators. Using a part decomposition algorithm for digitized 3D objects, represented as triangle meshes, we apply our shape measure to transform the low level mesh representation into a perceptually informative form. Further, we analyze the effects of noise, sensitivity to digitization, occlusions, and descriptiveness to demonstrate our shape measure on laser-scanned real world 3D objects. 1