Posterior shape models

We present a method to compute the conditional distribution of a statistical shape model given partial data. The result is a "posterior shape model", which is again a statistical shape model of the same form as the original model. This allows its direct use in the variety of algorithms that include prior knowledge about the variability of a class of shapes with a statistical shape model. Posterior shape models then provide a statistically sound yet easy method to integrate partial data into these algorithms. Usually, shape models represent a complete organ, for instance in our experiments the femur bone, modeled by a multivariate normal distribution. But because in many application certain parts of the shape are known a priori, it is of great interest to model the posterior distribution of the whole shape given the known parts. These could be isolated landmark points or larger portions of the shape, like the healthy part of a pathological or damaged organ. However, because for most shape models the dimensionality of the data is much higher than the number of examples, the normal distribution is singular, and the conditional distribution not readily available. In this paper, we present two main contributions: First, we show how the posterior model can be efficiently computed as a statistical shape model in standard form and used in any shape model algorithm. We complement this paper with a freely available implementation of our algorithms. Second, we show that most common approaches put forth in the literature to overcome this are equivalent to probabilistic principal component analysis (PPCA), and Gaussian Process regression. To illustrate the use of posterior shape models, we apply them on two problems from medical image analysis: model-based image segmentation incorporating prior knowledge from landmarks, and the prediction of anatomically correct knee shapes for trochlear dysplasia patients, which constitutes a novel medical application. Our experiments confirm that the use of conditional shape models for image segmentation improves the overall segmentation accuracy and robustness

Finite element surface registration incorporating curvature, volume preservation, and statistical model information

We present a novel method for nonrigid registration of 3D surfaces and images. The method can be used to register surfaces by means of their distance images, or to register medical images directly. It is formulated as a minimization problem of a sum of several terms representing the desired properties of a registration result: smoothness, volume preservation, matching of the surface, its curvature, and possible other feature images, as well as consistency with previous registration results of similar objects, represented by a statistical deformation model. While most of these concepts are already known, we present a coherent continuous formulation of these constraints, including the statistical deformation model. This continuous formulation renders the registration method independent of its discretization. The finite element discretization we present is, while independent of the registration functional, the second main contribution of this paper. The local discontinuous Galerkin method has not previously been used in image registration, and it provides an efficient and general framework to discretize each of the terms of our functional. Computational efficiency and modest memory consumption are achieved thanks to parallelization and locally adaptive mesh refinement. This allows for the first time the use of otherwise prohibitively large 3D statistical deformation models

Gaussian Process Morphable Models

Statistical shape models (SSMs) represent a class of shapes as a normal distribution of point variations, whose parameters are estimated from example shapes. Principal component analysis (PCA) is applied to obtain a low-dimensional representation of the shape variation in terms of the leading principal components. In this paper, we propose a generalization of SSMs, called Gaussian Process Morphable Models (GPMMs). We model the shape variations with a Gaussian process, which we represent using the leading components of its Karhunen-Loeve expansion. To compute the expansion, we make use of an approximation scheme based on the Nystrom method. The resulting model can be seen as a continuous analogon of an SSM. However, while for SSMs the shape variation is restricted to the span of the example data, with GPMMs we can define the shape variation using any Gaussian process. For example, we can build shape models that correspond to classical spline models, and thus do not require any example data. Furthermore, Gaussian processes make it possible to combine different models. For example, an SSM can be extended with a spline model, to obtain a model that incorporates learned shape characteristics, but is flexible enough to explain shapes that cannot be represented by the SSM. We introduce a simple algorithm for fitting a GPMM to a surface or image. This results in a non-rigid registration approach, whose regularization properties are defined by a GPMM. We show how we can obtain different registration schemes,including methods for multi-scale, spatially-varying or hybrid registration, by constructing an appropriate GPMM. As our approach strictly separates modelling from the fitting process, this is all achieved without changes to the fitting algorithm. We show the applicability and versatility of GPMMs on a clinical use case, where the goal is the model-based segmentation of 3D forearm images

Clionasterol, a triterpenoid from the Kenyan marine green macroalga halimeda macroloba

Peer reviewedPublisher PD

Dynamic Complexity of Formal Languages

The paper investigates the power of the dynamic complexity classes DynFO, DynQF and DynPROP over string languages. The latter two classes contain problems that can be maintained using quantifier-free first-order updates, with and without auxiliary functions, respectively. It is shown that the languages maintainable in DynPROP exactly are the regular languages, even when allowing arbitrary precomputation. This enables lower bounds for DynPROP and separates DynPROP from DynQF and DynFO. Further, it is shown that any context-free language can be maintained in DynFO and a number of specific context-free languages, for example all Dyck-languages, are maintainable in DynQF. Furthermore, the dynamic complexity of regular tree languages is investigated and some results concerning arbitrary structures are obtained: there exist first-order definable properties which are not maintainable in DynPROP. On the other hand any existential first-order property can be maintained in DynQF when allowing precomputation.Comment: Contains the material presenten at STACS 2009, extendes with proofs and examples which were omitted due lack of spac

Non-global logarithms in jet and isolation cone cross sections

Starting from a factorization theorem in effective field theory, we derive a parton-shower equation for the resummation of non-global logarithms. We have implemented this shower and interfaced it with a tree-level event generator to obtain an automated framework to resum the leading logarithm of non-global observables in the large-$N_c$ limit. Using this setup, we compute gap fractions for dijet processes and isolation cone cross sections relevant for photon production. We compare our results with fixed-order computations and LHC measurements. We find that naive exponentiation is often not adequate, especially when the vetoed region is small, since non-global contributions are enhanced due to their dependence on the veto-region size. Since our parton shower is derived from first principles and based on renormalization-group evolution, it is clear what ingredients will have to be included to perform resummations at subleading logarithmic accuracy in the future.Comment: 39 pages, 13 figures. v2: journal version with new result (4.18) for narrow isolation cone

Methodology and Code to Simulate Structural Change in SEAMLESS-IF: results for SEAMLESS test regions and integration into SEAMLESS-IF

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Productivity Analysis,

Report and Code to Simulate Structural Change

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use,