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A computed approximation of the solution operator to a system of partial differential equations (PDEs) is needed in various areas of science and engineering. Neural operators have been shown to be quite effective at predicting these solution generators after training on high-fidelity ground truth data (e.g. numerical simulations). However, in order to generalize well to unseen spatial domains, neural operators must be trained on an extensive amount of geometrically varying data samples that may not be feasible to acquire or simulate in certain contexts (e.g., patient-specific medical data, large-scale computationally intensive simulations.) We propose that in order to learn a PDE solution operator that can generalize across multiple domains without needing to sample enough data expressive enough for all possible geometries, we can train instead a latent neural operator on just a few ground truth solution fields diffeomorphically mapped from different geometric/spatial domains to a fixed reference configuration. Furthermore, the form of the solutions is dependent on the choice of mapping to and from the reference domain. We emphasize that preserving properties of the differential operator when constructing these mappings can significantly reduce the data requirement for achieving an accurate model due to the regularity of the solution fields that the latent neural operator is training on. We provide motivating numerical experimentation that demonstrates an extreme case of this consideration by exploiting the conformal invariance of the Laplacian

This paper introduces self-supervised neural network models to tackle several fundamental problems in the field of 3D human body analysis and processing. First, we propose VariShaPE (Varifold Shape Parameter Estimator), a novel architecture for the retrieval of latent space representations of body shapes and poses. This network offers a fast and robust method to estimate the embedding of arbitrary unregistered meshes into the latent space. Second, we complement the estimation of latent codes with MoGeN (Motion Geometry Network) a framework that learns the geometry on the latent space itself. This is achieved by lifting the body pose parameter space into a higher dimensional Euclidean space in which body motion mini-sequences from a training set of 4D data can be approximated by simple linear interpolation. Using the SMPL latent space representation we illustrate how the combination of these network models, once trained, can be used to perform a variety of tasks with very limited computational cost. This includes operations such as motion interpolation, extrapolation and transfer as well as random shape and pose generation., Comment: 23 pages, 11 figures, 6 tables

We introduce VISTA, a clustering approach for multivariate and irregularly sampled time series based on a parametric state space mixture model. VISTA is specifically designed for the unsupervised identification of groups in datasets originating from healthcare and psychology where such sampling issues are commonplace. Our approach adapts linear Gaussian state space models (LGSSMs) to provide a flexible parametric framework for fitting a wide range of time series dynamics. The clustering approach itself is based on the assumption that the population can be represented as a mixture of a given number of LGSSMs. VISTA's model formulation allows for an explicit derivation of the log-likelihood function, from which we develop an expectation-maximization scheme for fitting model parameters to the observed data samples. Our algorithmic implementation is designed to handle populations of multivariate time series that can exhibit large changes in sampling rate as well as irregular sampling. We evaluate the versatility and accuracy of our approach on simulated and real-world datasets, including demographic trends, wearable sensor data, epidemiological time series, and ecological momentary assessments. Our results indicate that VISTA outperforms most comparable standard times series clustering methods. We provide an open-source implementation of VISTA in Python.

Dynamical formulations of optimal transport (OT) frame the task of comparing distributions as a variational problem which searches for a path between distributions minimizing a kinetic energy functional. In applications, it is frequently natural to require paths of distributions to satisfy additional conditions. Inspired by this, we introduce a model for dynamical OT which incorporates constraints on the space of admissible paths into the framework of unbalanced OT, where the source and target measures are allowed to have a different total mass. Our main results establish, for several general families of constraints, the existence of solutions to the variational problem which defines this path constrained unbalanced optimal transport framework. These results are primarily concerned with distributions defined on a Euclidean space, but we extend them to distributions defined over parallelizable Riemannian manifolds as well. We also consider metric properties of our framework, showing that, for certain types of constraints, our model defines a metric on the relevant space of distributions. This metric is shown to arise as a geodesic distance of a Riemannian metric, obtained through an analogue of Otto's submersion in the classical OT setting., Comment: 23 pages, added reference to spherical Hellinger-Kantorovich

The solution of a PDE over varying initial/boundary conditions on multiple domains is needed in a wide variety of applications, but it is computationally expensive if the solution is computed de novo whenever the initial/boundary conditions of the domain change. We introduce a general operator learning framework, called DIffeomorphic Mapping Operator learNing (DIMON) to learn approximate PDE solutions over a family of domains $\{\Omega_{\theta}}_\theta$, that learns the map from initial/boundary conditions and domain $\Omega_\theta$ to the solution of the PDE, or to specified functionals thereof. DIMON is based on transporting a given problem (initial/boundary conditions and domain $\Omega_{\theta}$) to a problem on a reference domain $\Omega_{0}$, where training data from multiple problems is used to learn the map to the solution on $\Omega_{0}$, which is then re-mapped to the original domain $\Omega_{\theta}$. We consider several problems to demonstrate the performance of the framework in learning both static and time-dependent PDEs on non-rigid geometries; these include solving the Laplace equation, reaction-diffusion equations, and a multiscale PDE that characterizes the electrical propagation on the left ventricle. This work paves the way toward the fast prediction of PDE solutions on a family of domains and the application of neural operators in engineering and precision medicine.

This paper introduces a new mathematical and numerical framework for surface analysis derived from the general setting of elastic Riemannian metrics on shape spaces. Traditionally, those metrics are defined over the infinite dimensional manifold of immersed surfaces and satisfy specific invariance properties enabling the comparison of surfaces modulo shape preserving transformations such as reparametrizations. The specificity of the approach we develop is to restrict the space of allowable transformations to predefined finite dimensional bases of deformation fields. These are estimated in a data-driven way so as to emulate specific types of surface transformations observed in a training set. The use of such bases allows to simplify the representation of the corresponding shape space to a finite dimensional latent space. However, in sharp contrast with methods involving e.g. mesh autoencoders, the latent space is here equipped with a non-Euclidean Riemannian metric precisely inherited from the family of aforementioned elastic metrics. We demonstrate how this basis restricted model can be then effectively implemented to perform a variety of tasks on surface meshes which, importantly, does not assume these to be pre-registered (i.e. with given point correspondences) or to even have a consistent mesh structure. We specifically validate our approach on human body shape and pose data as well as human face scans, and show how it generally outperforms state-of-the-art methods on problems such as shape registration, interpolation, motion transfer or random pose generation., Comment: 18 pages, 10 figures, 8 tables

We present Basis Restricted Elastic Shape Analysis (BaRe-ESA), a novel Riemannian framework for human body scan representation, interpolation and extrapolation. BaRe-ESA operates directly on unregistered meshes, i.e., without the need to establish prior point to point correspondences or to assume a consistent mesh structure. Our method relies on a latent space representation, which is equipped with a Riemannian (non-Euclidean) metric associated to an invariant higher-order metric on the space of surfaces. Experimental results on the FAUST and DFAUST datasets show that BaRe-ESA brings significant improvements with respect to previous solutions in terms of shape registration, interpolation and extrapolation. The efficiency and strength of our model is further demonstrated in applications such as motion transfer and random generation of body shape and pose., Comment: 13 pages, 7 figures, 3 tables

This paper introduces a new framework for non-parallel emotion conversion in speech. Our framework is based on two key contributions. First, we propose a stochastic version of the popular CycleGAN model. Our modified loss function introduces a Kullback Leibler (KL) divergence term that aligns the source and target data distributions learned by the generators, thus overcoming the limitations of sample wise generation. By using a variational approximation to this stochastic loss function, we show that our KL divergence term can be implemented via a paired density discriminator. We term this new architecture a variational CycleGAN (VCGAN). Second, we model the prosodic features of target emotion as a smooth and learnable deformation of the source prosodic features. This approach provides implicit regularization that offers key advantages in terms of better range alignment to unseen and out of distribution speakers. We conduct rigorous experiments and comparative studies to demonstrate that our proposed framework is fairly robust with high performance against several state-of-the-art baselines., Comment: Accepted in IEEE Transactions on Audio, Speech and Language Processing

A main goal in the field of statistical shape analysis is to define computable and informative metrics on spaces of immersed manifolds, such as the space of curves in a Euclidean space. The approach taken in the elastic shape analysis framework is to define such a metric by starting with a reparameterization-invariant Riemannian metric on the space of parameterized shapes and inducing a metric on the quotient by the group of diffeomorphisms. This quotient metric is computed, in practice, by finding a registration of two shapes over the diffeomorphism group. For spaces of Euclidean curves, the initial Riemannian metric is frequently chosen from a two-parameter family of Sobolev metrics, called elastic metrics. Elastic metrics are especially convenient because, for several parameter choices, they are known to be locally isometric to Riemannian metrics for which one is able to solve the geodesic boundary problem explictly -- well-known examples of these local isometries include the complex square root transform of Younes, Michor, Mumford and Shah and square root velocity (SRV) transform of Srivastava, Klassen, Joshi and Jermyn. In this paper, we show that the SRV transform extends to elastic metrics for all choices of parameters, for curves in any dimension, thereby fully generalizing the work of many authors over the past two decades. We give a unified treatment of the elastic metrics: we extend results of Trouv\'{e} and Younes, Bruveris as well as Lahiri, Robinson and Klassen on the existence of solutions to the registration problem, we develop algorithms for computing distances and geodesics, and we apply these algorithms to metric learning problems, where we learn optimal elastic metric parameters for statistical shape analysis tasks.

This paper reviews several Riemannian metrics and evolution equations in the context of diffeomorphic shape analysis. After a short review of of various approaches at building Riemannian spaces of shapes, with a special focus on the foundations of the large deformation diffeomorphic metric mapping algorithm, the attention is turned to elastic metrics, and to growth models that can be derived from it. In the latter context, a new class of metrics, involving the optimization of a growth tensor, is introduced and some of its properties are studied., Comment: 25 pages, 5 figures

This paper introduces a set of numerical methods for Riemannian shape analysis of 3D surfaces within the setting of invariant (elastic) second-order Sobolev metrics. More specifically, we address the computation of geodesics and geodesic distances between parametrized or unparametrized immersed surfaces represented as 3D meshes. Building on this, we develop tools for the statistical shape analysis of sets of surfaces, including methods for estimating Karcher means and performing tangent PCA on shape populations, and for computing parallel transport along paths of surfaces. Our proposed approach fundamentally relies on a relaxed variational formulation for the geodesic matching problem via the use of varifold fidelity terms, which enable us to enforce reparametrization independence when computing geodesics between unparametrized surfaces, while also yielding versatile algorithms that allow us to compare surfaces with varying sampling or mesh structures. Importantly, we demonstrate how our relaxed variational framework can be extended to tackle partially observed data. The different benefits of our numerical pipeline are illustrated over various examples, synthetic and real., Comment: 28 pages, 16 figures, 2 tables

This paper introduces and studies a metamorphosis framework for geometric measures known as varifolds, which extends the diffeomorphic registration model for objects such as curves, surfaces and measures by complementing diffeomorphic deformations with a transformation process on the varifold weights. We consider two classes of cost functionals to penalize those combined transformations, in particular the LDDMM-Fisher-Rao energy which, as we show, leads to a well-defined Riemannian metric on the space of varifolds with existence of corresponding geodesics. We further introduce relaxed formulations of the respective optimal control problems, study their well-posedness and derive optimality conditions for the solutions. From these, we propose a numerical approach to compute optimal metamorphoses between discrete varifolds and illustrate the interest of this model in the situation of partially missing data.

This paper introduces a new extension of Riemannian elastic curve matching to a general class of geometric structures, which we call (weighted) shape graphs, that allows for shape registration with partial matching constraints and topological inconsistencies. Weighted shape graphs are the union of an arbitrary number of component curves in Euclidean space with potential connectivity constraints between some of their boundary points, together with a weight function defined on each component curve. The framework of higher order invariant Sobolev metrics is particularly well suited for constructing notions of distances and geodesics between unparametrized curves. The main difficulty in adapting this framework to the setting of shape graphs is the absence of topological consistency, which typically results in an inadequate search for an exact matching between two shape graphs. We overcome this hurdle by defining an inexact variational formulation of the matching problem between (weighted) shape graphs of any underlying topology, relying on the convenient measure representation given by varifolds to relax the exact matching constraint. We then prove the existence of minimizers to this variational problem when we choose Sobolev metrics of sufficient regularity and a total variation (TV) regularization on the weight function. We propose a numerical optimization approach which adapts the smoothed fast iterative shrinkage-thresholding (SFISTA) algorithm to deal with TV norm minimization and allows us to reduce the matching problem to solving a sequence of smooth unconstrained minimization problems. We finally illustrate the capabilities of our new model through several examples showcasing its ability to tackle partially observed and topologically varying data., Comment: 29 pages, 8 figures

This paper studies a longitudinal shape transformation model in which shapes are deformed in response to an internal growth potential that evolves according to an advection reaction diffusion process. This model extends prior works that considered a static growth potential, i.e., the initial growth potential is only advected by diffeomorphisms. We focus on the mathematical study of the corresponding system of coupled PDEs describing the joint dynamics of the diffeomorphic transformation together with the growth potential on the moving domain. Specifically, we prove the uniqueness and long time existence of solutions to this system with reasonable initial and boundary conditions as well as regularization on deformation fields. In addition, we provide a few simple simulations of this model in the case of isotropic elastic materials in 2D., Comment: 31 pages, 4 figures

Motivated by applications from computer vision to bioinformatics, the field of shape analysis deals with problems where one wants to analyze geometric objects, such as curves, while ignoring actions that preserve their shape, such as translations, rotations, or reparametrizations. Mathematical tools have been developed to define notions of distances, averages, and optimal deformations for geometric objects. One such framework, which has proven to be successful in many applications, is based on the square root velocity (SRV) transform, which allows one to define a computable distance between spatial curves regardless of how they are parametrized. This paper introduces a supervised deep learning framework for the direct computation of SRV distances between curves, which usually requires an optimization over the group of reparametrizations that act on the curves. The benefits of our approach in terms of computational speed and accuracy are illustrated via several numerical experiments., Comment: 8 pages, 7 figures, 3 tables. Accepted to DiffCVML

In this paper, we revisit the notion of length measures associated to planar closed curves. These are a special case of area measures of hypersurfaces which were introduced early on in the field of convex geometry. The length measure of a curve is a measure on the circle $\mathbb{S}^1$ that intuitively represents the length of the portion of curve which tangent vector points in a certain direction. While a planar closed curve is not characterized by its length measure, the fundamental Minkowski-Fenchel-Jessen theorem states that length measures fully characterize convex curves modulo translations, making it a particularly useful tool in the study of geometric properties of convex objects. The present work, that was initially motivated by problems in shape analysis, introduces length measures for the general class of Lipschitz immersed and oriented planar closed curves, and derives some of the basic properties of the length measure map on this class of curves. We then focus specifically on the case of convex shapes and present several new results. First, we prove an isoperimetric characterization of the unique convex curve associated to some length measure given by the Minkowski-Fenchel-Jessen theorem, namely that it maximizes the signed area among all the curves sharing the same length measure. Second, we address the problem of constructing a distance with associated geodesic paths between convex planar curves. For that purpose, we introduce and study a new distance on the space of length measures that corresponds to a constrained variant of the Wasserstein metric of optimal transport, from which we can induce a distance between convex curves. We also propose a primal-dual algorithm to numerically compute those distances and geodesics, and show a few simple simulations to illustrate the approach., Comment: 30 pages, 10 figures

We propose a novel method for emotion conversion in speech based on a chained encoder-decoder-predictor neural network architecture. The encoder constructs a latent embedding of the fundamental frequency (F0) contour and the spectrum, which we regularize using the Large Diffeomorphic Metric Mapping (LDDMM) registration framework. The decoder uses this embedding to predict the modified F0 contour in a target emotional class. Finally, the predictor uses the original spectrum and the modified F0 contour to generate a corresponding target spectrum. Our joint objective function simultaneously optimizes the parameters of three model blocks. We show that our method outperforms the existing state-of-the-art approaches on both, the saliency of emotion conversion and the quality of resynthesized speech. In addition, the LDDMM regularization allows our model to convert phrases that were not present in training, thus providing evidence for out-of-sample generalization., Comment: Paper Accepted in Interspeech 2020

Surface comparison and matching is a challenging problem in computer vision. While reparametrization-invariant Sobolev metrics provide meaningful elastic distances and point correspondences via the geodesic boundary value problem, solving this problem numerically tends to be difficult. Square root normal fields (SRNF) considerably simplify the computation of certain elastic distances between parametrized surfaces. Yet they leave open the issue of finding optimal reparametrizations, which induce elastic distances between unparametrized surfaces. This issue has concentrated much effort in recent years and led to the development of several numerical frameworks. In this paper, we take an alternative approach which bypasses the direct estimation of reparametrizations: we relax the geodesic boundary constraint using an auxiliary parametrization-blind varifold fidelity metric. This reformulation has several notable benefits. By avoiding altogether the need for reparametrizations, it provides the flexibility to deal with simplicial meshes of arbitrary topologies and sampling patterns. Moreover, the problem lends itself to a coarse-to-fine multi-resolution implementation, which makes the algorithm scalable to large meshes. Furthermore, this approach extends readily to higher-order feature maps such as square root curvature fields and is also able to include surface textures in the matching problem. We demonstrate these advantages on several examples, synthetic and real., Comment: 21 pages, 11 figures, 1 table, 3 algorithms. Forthcoming in the International Journal of Computer Vision

This chapter reviews some past and recent developments in shape comparison and analysis of curves based on the computation of intrinsic Riemannian metrics on the space of curves modulo shape-preserving transformations. We summarize the general construction and theoretical properties of quotient elastic metrics for Euclidean as well as non-Euclidean curves before considering the special case of the square root velocity metric for which the expression of the resulting distance simplifies through a particular transformation. We then examine different numerical approaches that have been proposed to estimate such distances in practice and in particular to quotient out curve reparametrization in the resulting minimization problems., Comment: 25 pages, 4 figures

This paper examines a longitudinal shape evolution model in which a 3D volume progresses through a family of elastic equilibria in response to the time-derivative of an internal force, or yank, with an additional regularization to ensure diffeomorphic transformations. We consider two different models of yank and address the long time existence and uniqueness of solutions for the equations of motion in both models. In addition, we derive sufficient conditions for the existence of an optimal yank that best describes the change from an observed initial volume to an observed volume at a later time. The main motivation for this work is the understanding of processes such as growth and atrophy in anatomical structures, where the yank could be roughly interpreted as a metabolic event triggering morphological changes. We provide preliminary results on simple examples to illustrate, under this model, the retrievability of some attributes of such events., Comment: 41 pages, 11 figures

This paper introduces a new mathematical formulation and numerical approach for the computation of distances and geodesics between immersed planar curves. Our approach combines the general simplifying transform for first-order elastic metrics that was recently introduced by Kurtek and Needham, together with a relaxation of the matching constraint using parametrization-invariant fidelity metrics. The main advantages of this formulation are that it leads to a simple optimization problem for discretized curves, and that it provides a flexible approach to deal with noisy, inconsistent or corrupted data. These benefits are illustrated via a few preliminary numerical results., Comment: 5 pages, 5 figures

This paper is concerned with the theory and applications of varifolds to the representation, approximation and diffeomorphic registration of shapes. One of its purpose is to synthesize and extend several prior works which, so far, have made use of this framework mainly in the context of submanifold comparison and matching. In this work, we instead consider deformation models acting on general varifold spaces, which allows to formulate and tackle diffeomorphic registration problems for a much wider class of geometric objects and lead to a more versatile algorithmic pipeline. We study in detail the construction of kernel metrics on varifold spaces and the resulting topological properties of those metrics, then propose a mathematical model for diffeomorphic registration of varifolds under a specific group action which we formulate in the framework of optimal control theory. A second important part of the paper focuses on the discrete aspects. Specifically, we address the problem of optimal finite approximations (quantization) for those metrics and show a $\Gamma$-convergence property for the corresponding registration functionals. Finally, we develop numerical pipelines for quantization and registration before showing a few preliminary results for one and two-dimensional varifolds.

This paper puts forth a new formulation and algorithm for the elastic matching problem on unparametrized curves and surfaces. Our approach combines the frameworks of square root normal fields and varifold fidelity metrics into a novel framework, which has several potential advantages over previous works. First, our variational formulation allows us to minimize over reparametrizations without discretizing the reparametrization group. Second, the objective function and gradient are easy to implement and efficient to evaluate numerically. Third, the initial and target surface may have different samplings and even different topologies. Fourth, texture can be incorporated as additional information in the matching term similarly to the fshape framework. We demonstrate the usefulness of this approach with several numerical examples of curves and surfaces., Comment: 7 pages, 4 figures

We study a shape evolution framework in which the deformation of shapes from time t to t + dt is governed by a regularized anisotropic elasticity model. More precisely, we assume that at each time shapes are infinitesimally deformed from a stress-free state to an elastic equilibrium as a result of the application of a small force. The configuration of equilibrium then becomes the new resting state for subsequent evolution. The primary motivation of this work is the modeling of slow changes in biological shapes like atrophy, where a body force applied to the volume represents the location and impact of the disease. Our model uses an optimal control viewpoint with the time derivative of force interpreted as a control, deforming a shape gradually from its observed initial state to an observed final state. Furthermore, inspired by the layered organization of cortical volumes, we consider a special case of our model in which shapes can be decomposed into a family of layers (forming a "foliation"). Preliminary experiments on synthetic layered shapes in two and three dimensions are presented to demonstrate the effect of elasticity., Comment: 12 pages, 6 figures

These are the proceedings of the workshop "Math in the Black Forest", which brought together researchers in shape analysis to discuss promising new directions. Shape analysis is an inter-disciplinary area of research with theoretical foundations in infinite-dimensional Riemannian geometry, geometric statistics, and geometric stochastics, and with applications in medical imaging, evolutionary development, and fluid dynamics. The workshop is the 6th instance of a series of workshops on the same topic., Comment: 27 pages, 4 figures

This paper presents an overview of recent developments in the analysis of shapes such as curves and surfaces through Riemannian metrics. We show that several constructions of metrics on spaces of submanifolds can be unified through the prism of Riemannian submersions, with shape space metrics being induced from metrics defined on the top spaces. Computing the resulting Riemannian distances involves solving geodesic matching problems with boundary conditions. To deal efficiently with such variational problems, one can rely on an auxiliary family of "chordal" distances to simplify the treatment of boundary conditions, which we use to come up with a relaxed inexact formulation of the matching problem. This also allows to turn shape matching into optimal control problems and give a common framework to address them in practice. We then specify our analysis to the cases of intrinsic shape metrics defined using invariant Sobolev metrics on parametrized immersions, outer shape metrics induced from metrics on diffeomorphism groups of the ambient space and finally a recent hybrid model that combines those two approaches., Comment: 28 pages, 5 figures

Sparse dictionary learning is a popular method for representing signals as linear combinations of a few elements from a dictionary that is learned from the data. In the classical setting, signals are represented as vectors and the dictionary learning problem is posed as a matrix factorization problem where the data matrix is approximately factorized into a dictionary matrix and a sparse matrix of coefficients. However, in many applications in computer vision and medical imaging, signals are better represented as matrices or tensors (e.g. images or videos), where it may be beneficial to exploit the multi-dimensional structure of the data to learn a more compact representation. One such approach is separable dictionary learning, where one learns separate dictionaries for different dimensions of the data. However, typical formulations involve solving a non-convex optimization problem; thus guaranteeing global optimality remains a challenge. In this work, we propose a framework that builds upon recent developments in matrix factorization to provide theoretical and numerical guarantees of global optimality for separable dictionary learning. We propose an algorithm to find such a globally optimal solution, which alternates between following local descent steps and checking a certificate for global optimality. We illustrate our approach on diffusion magnetic resonance imaging (dMRI) data, a medical imaging modality that measures water diffusion along multiple angular directions in every voxel of an MRI volume. State-of-the-art methods in dMRI either learn dictionaries only for the angular domain of the signals or in some cases learn spatial and angular dictionaries independently. In this work, we apply the proposed separable dictionary learning framework to learn spatial and angular dMRI dictionaries jointly and provide preliminary validation on denoising phantom and real dMRI brain data.

In this paper we study a class of Riemannian metrics on the space of unparametrized curves and develop a method to compute geodesics with given boundary conditions. It extends previous works on this topic in several important ways. The model and resulting matching algorithm integrate within one common setting both the family of $H^2$-metrics with constant coefficients and scale-invariant $H^2$-metrics on both open and closed immersed curves. These families include as particular cases the class of first-order elastic metrics. An essential difference with prior approaches is the way that boundary constraints are dealt with. By leveraging varifold-based similarity metrics we propose a relaxed variational formulation for the matching problem that avoids the necessity of optimizing over the reparametrization group. Furthermore, we show that we can also quotient out finite-dimensional similarity groups such as translation, rotation and scaling groups. The different properties and advantages are illustrated through numerical examples in which we also provide a comparison with related diffeomorphic methods used in shape registration., Comment: 27 pages

This paper proposes a new framework and algorithms to address the problem of diffeomorphic registration on a general class of geometric objects that can be described as discrete distributions of local direction vectors. It builds on both the large deformation diffeomorphic metric mapping (LDDMM) model and the concept of oriented varifolds introduced in previous works like [Kaltenmark 2017]. Unlike previous approaches in which varifold representations are only used as surrogates to define and evaluate fidelity terms, the specificity of this paper is to derive direct deformation models and corresponding matching algorithms for discrete varifolds. We show that it gives on the one hand an alternative numerical setting for curve and surface matching but that it can also handle efficiently more general shape structures, including multi-directional objects or multi-modal images represented as distributions of unit gradient vectors.

Advanced diffusion magnetic resonance imaging (dMRI) techniques, like diffusion spectrum imaging (DSI) and high angular resolution diffusion imaging (HARDI), remain underutilized compared to diffusion tensor imaging because the scan times needed to produce accurate estimations of fiber orientation are significantly longer. To accelerate DSI and HARDI, recent methods from compressed sensing (CS) exploit a sparse underlying representation of the data in the spatial and angular domains to undersample in the respective k- and q-spaces. State-of-the-art frameworks, however, impose sparsity in the spatial and angular domains separately and involve the sum of the corresponding sparse regularizers. In contrast, we propose a unified (k,q)-CS formulation which imposes sparsity jointly in the spatial-angular domain to further increase sparsity of dMRI signals and reduce the required subsampling rate. To efficiently solve this large-scale global reconstruction problem, we introduce a novel adaptation of the FISTA algorithm that exploits dictionary separability. We show on phantom and real HARDI data that our approach achieves significantly more accurate signal reconstructions than the state of the art while sampling only 2-4% of the (k,q)-space, allowing for the potential of new levels of dMRI acceleration., Comment: To be published in the 2017 Computational Diffusion MRI Workshop of MICCAI

Second order Sobolev metrics are a useful tool in the shape analysis of curves. In this paper we combine these metrics with varifold-based inexact matching to explore a new strategy of computing geodesics between unparametrized curves. We describe the numerical method used for solving the inexact matching problem, apply it to study the shape of mosquito wings and compare our method to curve matching in the LDDMM framework., Comment: 12 pages

Diffusion MRI (dMRI) provides the ability to reconstruct neuronal fibers in the brain, $\textit{in vivo}$, by measuring water diffusion along angular gradient directions in q-space. High angular resolution diffusion imaging (HARDI) can produce better estimates of fiber orientation than the popularly used diffusion tensor imaging, but the high number of samples needed to estimate diffusivity requires longer patient scan times. To accelerate dMRI, compressed sensing (CS) has been utilized by exploiting a sparse dictionary representation of the data, discovered through sparse coding. The sparser the representation, the fewer samples are needed to reconstruct a high resolution signal with limited information loss, and so an important area of research has focused on finding the sparsest possible representation of dMRI. Current reconstruction methods however, rely on an angular representation $\textit{per voxel}$ with added spatial regularization, and so, for non-zero signals, one is required to have at least one non-zero coefficient per voxel. This means that the global level of sparsity must be greater than the number of voxels. In contrast, we propose a joint spatial-angular representation of dMRI that will allow us to achieve levels of global sparsity that are below the number of voxels. A major challenge, however, is the computational complexity of solving a global sparse coding problem over large-scale dMRI. In this work, we present novel adaptations of popular sparse coding algorithms that become better suited for solving large-scale problems by exploiting spatial-angular separability. Our experiments show that our method achieves significantly sparser representations of HARDI than is possible by the state of the art.

CLARITY is a method for converting biological tissues into translucent and porous hydrogel-tissue hybrids. This facilitates interrogation with light sheet microscopy and penetration of molecular probes while avoiding physical slicing. In this work, we develop a pipeline for registering CLARIfied mouse brains to an annotated brain atlas. Due to the novelty of this microscopy technique it is impractical to use absolute intensity values to align these images to existing standard atlases. Thus we adopt a large deformation diffeomorphic approach for registering images via mutual information matching. Furthermore we show how a cascaded multi-resolution approach can improve registration quality while reducing algorithm run time. As acquired image volumes were over a terabyte in size, they were far too large for work on personal computers. Therefore the NeuroData computational infrastructure was deployed for multi-resolution storage and visualization of these images and aligned annotations on the web.

In this paper, we describe in detail a model of geometric-functional variability between fshapes. These objects were introduced for the first time by the authors in [Charlier et al. 2015] and are basically the combination of classical deformable manifolds with additional scalar signal map. Building on the aforementioned work, this paper's contributions are several. We first extend the original $L^2$ model in order to represent signals of higher regularity on their geometrical support with more regular Hilbert norms (typically Sobolev). We describe the bundle structure of such fshape spaces with their adequate geodesic distances, encompassing in one common framework usual shape comparison and image metamorphoses. We then propose a formulation of matching between any two fshapes from the optimal control perspective, study existence of optimal controls and derive Hamiltonian equations and conservation laws describing the dynamics of geodesics. Secondly, we tackle the discrete counterpart of these problems and equations through appropriate finite elements interpolation schemes on triangular meshes. At last, we show a few results of metamorphosis matchings on synthetic and several real data examples in order to highlight the key specificities of the approach., Comment: 46 pages, 12 figures

The CLARITY method renders brains optically transparent to enable high-resolution imaging in the structurally intact brain. Anatomically annotating CLARITY brains is necessary for discovering which regions contain signals of interest. Manually annotating whole-brain, terabyte CLARITY images is difficult, time-consuming, subjective, and error-prone. Automatically registering CLARITY images to a pre-annotated brain atlas offers a solution, but is difficult for several reasons. Removal of the brain from the skull and subsequent storage and processing cause variable non-rigid deformations, thus compounding inter-subject anatomical variability. Additionally, the signal in CLARITY images arises from various biochemical contrast agents which only sparsely label brain structures. This sparse labeling challenges the most commonly used registration algorithms that need to match image histogram statistics to the more densely labeled histological brain atlases. The standard method is a multiscale Mutual Information B-spline algorithm that dynamically generates an average template as an intermediate registration target. We determined that this method performs poorly when registering CLARITY brains to the Allen Institute's Mouse Reference Atlas (ARA), because the image histogram statistics are poorly matched. Therefore, we developed a method (Mask-LDDMM) for registering CLARITY images, that automatically find the brain boundary and learns the optimal deformation between the brain and atlas masks. Using Mask-LDDMM without an average template provided better results than the standard approach when registering CLARITY brains to the ARA. The LDDMM pipelines developed here provide a fast automated way to anatomically annotate CLARITY images. Our code is available as open source software at http://NeuroData.io.

This article introduces a full mathematical and numerical framework for treating functional shapes (or fshapes) following the landmarks of shape spaces and shape analysis. Functional shapes can be described as signal functions supported on varying geometrical supports. Analysing variability of fshapes' ensembles require the modelling and quantification of joint variations in geometry and signal, which have been treated separately in previous approaches. Instead, building on the ideas of shape spaces for purely geometrical objects, we propose the extended concept of fshape bundles and define Riemannian metrics for fshape metamorphoses to model geometrico-functional transformations within these bundles. We also generalize previous works on data attachment terms based on the notion of varifolds and demonstrate the utility of these distances. Based on these, we propose variational formulations of the atlas estimation problem on populations of fshapes and prove existence of solutions for the different models. The second part of the article examines the numerical implementation of the models by detailing discrete expressions for the metrics and gradients and proposing an optimization scheme for the atlas estimation problem. We present a few results of the methodology on a synthetic dataset as well as on a population of retinal membranes with thickness maps.

In this paper, we address the problem of orientation that naturally arises when representing shapes like curves or surfaces as currents. In the field of computational anatomy, the framework of currents has indeed proved very efficient to model a wide variety of shapes. However, in such approaches, orientation of shapes is a fundamental issue that can lead to several drawbacks in treating certain kind of datasets. More specifically, problems occur with structures like acute pikes because of canceling effects of currents or with data that consists in many disconnected pieces like fiber bundles for which currents require a consistent orientation of all pieces. As a promising alternative to currents, varifolds, introduced in the context of geometric measure theory by F. Almgren, allow the representation of any non-oriented manifold (more generally any non-oriented rectifiable set). In particular, we explain how varifolds can encode numerically non-oriented objects both from the discrete and continuous point of view. We show various ways to build a Hilbert space structure on the set of varifolds based on the theory of reproducing kernels. We show that, unlike the currents' setting, these metrics are consistent with shape volume (theorem 4.1) and we derive a formula for the variation of metric with respect to the shape (theorem 4.2). Finally, we propose a generalization to non-oriented shapes of registration algorithms in the context of Large Deformations Metric Mapping (LDDMM), which we detail with a few examples in the last part of the paper., Comment: 33 pages, 10 figures