Statistical Shape Modeling

Perceiving structured shapes, such as human faces, from pixels is an inherently ambiguous task in real-world conditions. Yet, shape inference is largely posed as a deterministic regression task predicting fixed spatial coordinates. We find that deterministic regression is brittle when visual evidence is ambiguous or incomplete; under severe occlusions deterministic models exhibit structural collapse, predicting incoherent shapes or reverting to generic averages. To address this, we introduce Shape-Bayes, a probabilistic framework that couples uncertainty-aware visual perception with Bayesian shape reasoning. Rather than forcing point estimates, Shape-Bayes dynamically weights visual evidence against geometric priors to infer a structurally valid shape posterior. Demonstrated on human face shape regression, a rigorous testbed featuring complex non-rigid deformations and strict anatomical constraints, Shape-Bayes comprises: (1) a base model predicting noisy landmarks alongside distilled aleatoric uncertainties; (2) a lightweight Transformer encoding these observations into an adaptive prior over a PCA shape manifold; and (3) a differentiable Bayesian solver computing closed-form posteriors by balancing the noisy predictions against this prior. By guaranteeing complete structural integrity, Shape-Bayes achieves an absolute improvement of up to ~34% IDR over state-of-the-art deterministic models. Simultaneously, it yields highly calibrated uncertainty bounds and reduces relative error by up to 12.5%, establishing a new state-of-the-art for robust 2D face shape regression under severe occlusion. The project page is at https://shape-bayes.github.io.

The corpus callosum (CC) is a major white-matter structure and a well-established marker of brain aging, but most studies quantify it using scalar summaries that discard its boundary geometry. We present a Riemannian shape-space framework for analyzing age-related morphological change in the midsagittal CC, applied to the OASIS-1 cohort. Each contour is represented by $128$ landmarks and embedded into Kendall shape space, where translation, rotation, and scale are removed. We derive a multivariate geodesic regression with exact Riemannian gradients and use the fitted age-velocity field to localize age-related deformation to five anatomical sub-regions. In the cognitively normal cohort ($n = 252$), geodesic regression outperforms the Euclidean linear benchmark ($R^2 = 0.1355$ vs.\ $0.1216$). Regional energy is posterior-dominant: the Splenium carries $41.4\%$ and the Isthmus $23.8\%$ of total age-related shape change, together accounting for $\sim 65\%$ despite comprising only $\sim 35\%$ of landmarks. Signed projections confirm the ordering (Splenium $r = 0.570$; Isthmus $r = 0.473$). In contrast, age explains less than $0.5\%$ of shape variance in Alzheimer's disease ($n = 88$), indicating that the disease disrupts the healthy aging trajectory. A tangent-space classifier achieves an age-group AUC of $0.791$ from the 2D contour alone, exceeding a recent volumetric benchmark ($0.67$).

Quantitative characterization of lymph node morphology is important for assessing axillary lymph node metastasis in breast cancer. However, surfaces reconstructed from computed tomography (CT) segmentation may contain geometric and topological defects that compromise subsequent analysis, while conventional shape descriptors predominantly characterize global morphology. To address these issues, we developed an integrated framework combining topology-aware surface processing with multi-resolution spherical harmonic (SH) analysis of CT-derived axillary lymph nodes. The processing pipeline produced topology-valid genus-0 surfaces with improved mesh quality, which were then represented at multiple SH degrees and characterized using 20 predefined geometric feature families. Geometric fidelity increased with SH degree, whereas predictive performance peaked at intermediate resolutions. Preferred SH degree also differed across feature families. A family-specific mixed-resolution model achieved an AUC of 0.918, compared with 0.884 for the conventional PyRadiomics Shape14 baseline, corresponding to an improvement of 0.0344. Controlled perturbation experiments showed that higher SH degrees transmitted more fine-scale geometric variation and yielded lower stability of curvature-based predictions. Representative geometric descriptors provided interpretable characterization of metastasis-associated surface morphology. Independent validation further supported the framework's transportability: label-free replication in a multicenter lymph node cohort reproduced the family-specific resolution effects, while a labeled LIDC-IDRI lung-nodule experiment reproduced the resolution-dependent relationship between SH degree and predictive performance. Altogether, the framework provides a topology-valid basis for quantitative characterization of lymph node morphology and metastasis-associated imaging phenotypes.

We introduce NeuralSRNF, a novel framework for the statistical shape analysis and generation of genus-zero 3D and 4D objects that undergo nonrigid deformations. Traditional methods rely on complex and computationally expensive nonlinear elastic metrics that measure bending and stretching. Recent advances in elastic shape analysis achieve computational efficiency by mapping input 3D shapes to the space of Square Root Normal Fields (SRNFs) where the L2 metric approximates the partial elastic metric, significantly facilitating the process of computing geodesics and summary statistics. SRNFs, however, are not invertible, and the numerical algorithms used to map SRNFs back to the original space of surfaces remain computationally very expensive and often lead to approximate results. This paper addresses this fundamental SRNF inversion problem using a novel neural representation, termed NeuralSRNF. Unlike the commonly used numerical SRNF, NeuralSRNF is (1) continuous, and thus resolution-agnostic, enabling full functional shape analysis, (2) more accurate, and (3) computationally more efficient as it can compute inverse SRNF maps along a geodesic path in less than 3 s compared to over 10 min for the numerical SRNF. We demonstrate, using various datasets, the utility and efficiency of the proposed NeuralSRNF in multiple elastic 3D and 4D shape analysis tasks such as geodesic computation, deformation transfer, statistical summaries computation, and 3D shape generation. We show that it outperforms competing methods on most evaluated datasets and metrics by a wide margin in both accuracy and computational efficiency. The source code and additional results are available at https://awaisnizamani16.github.io/awais/NeuralSRNF/.

Sparse-view X-ray 3D reconstruction is essential for reducing radiation exposure, but recovering a density field from a handful of X-ray projections is severely ill-posed. Recently, 3D Gaussian Splatting has achieved state-of-the-art performance in sparse-view reconstruction by representing the volume using explicit, optimized primitives, but it requires dozens of projected views. With fewer views, reconstruction quality degrades severely since the explicit primitives are optimized freely without any anatomical information. Anatomical structures, in contrast, share similar geometry and density across a population. Their variations are bounded within a limited range that statistical shape models can capture. This paper proposes a shape-guided Gaussian splatting framework for sparse-view X-ray 3D reconstructions. Our contribution lies in driving Gaussian positions toward anatomically valid configurations, alongside atlas-based density regularization. Our method ensures anatomically consistent reconstruction and improves PSNR by 2.83 dB over a state-of-the-art Gaussian splatting baseline with as few as 5 views. Code Available: https://github.com/polyshape-lab/ShapeGuidedGaussian

Three-dimensional femoral reconstruction from radiographs supports surgical planning, implant sizing, and post-operative follow-up, but remains ill-posed as X-ray projections discard depth information. Existing methods often incorporate a 3D statistical shape model (SSM) as a shape prior to guide reconstructions toward anatomically plausible shapes, relying on iterative 3D-to-2D projection matching. Yet, these approaches are computationally expensive and constrain their SSM to a single dimensionality, leaving the statistical relationship between 2D observations and 3D geometry largely unexploited and unexplored. We instead propose a joint 2D-3D SSM that explicitly captures the co-variation between 2D and 3D segmentations in a shared latent space. During training, 2D and 3D segmentations are registered to a common 3D template and its corresponding 2D projections, and the resulting stationary velocity fields are jointly decomposed using principal component analysis (PCA). This joint modeling allows the 2D-to-3D mapping to be learned directly from data rather than computing correspondences at inference time. For unseen subjects, the 3D shape is recovered directly by lifting the 2D latent coordinates to the 3D PCA subspace, thereby eliminating the need for iterative 3D-to-2D projection. Experiments on NMDID demonstrate that the proposed joint 2D-3D SSM outperforms a widely-used 3D-only SSM baseline while achieving inference approximately 4 times faster, at under 3 seconds per subject. The code is available at: https://github.com/florence-dellaniello-picard/joint2d3d-ssm.

This paper introduces Mixtures of Geodesic Factor Analyzers (MGFA) on Riemannian homogeneous spaces. MGFA uses a geodesic factor model within each mixture component, providing greater expressiveness than mixtures of Riemannian radial distributions and enabling clustering of manifold-valued data with anisotropic subpopulations. We establish root-$n$ consistency for the MGFA maximum likelihood estimator (MLE), thereby filling a theoretical gap for mixtures of Riemannian radial distributions as a special case. We also propose an iterative estimation algorithm and implement it on spheres, shape spaces, and hyperbolic spaces. Numerical experiments show that MGFA substantially outperforms competing methods in well-specified regimes while remaining robust under model misspecification. Finally, case studies on corpus callosum and left hippocampus shape datasets demonstrate MGFA's effectiveness for both 2D contour and 3D shape analysis.

Correspondence-based statistical shape modeling (SSM) is vital for population-level morphometric analysis, but conventional pipelines assume clean, fully registered surfaces. Real-world clinical photogrammetry scans are often noisy, partial, and cluttered, hindering the adoption of radiation-free surface imaging as a safe alternative to computed tomography (CT) for infant craniosynostosis. We present SCALP (Semi-supervised Correspondence via lAndmark Localization and sPectral warping), a two-stage framework that constructs consistent shape models directly from raw, imperfect surface scans. First, a semi-supervised Point Transformer leverages a small expert-annotated dataset alongside a large unlabeled cohort to accurately localize craniofacial landmarks with minimal annotation overhead. Second, these landmarks anchor a Laplace--Beltrami spectral deformation of an anatomical template, generating dense correspondences while naturally isolating the cranium from peripheral scanning clutter without manual preprocessing. Experiments on infant photogrammetry scans demonstrate that SCALP consistently outperforms state-of-the-art unsupervised point-cloud approaches, offering a clinically practical pathway toward objective, radiation-free head shape analysis.

The shape of a planar curve is the geometric information that remains once translation, rotation, scale and reparametrisation are removed and is of interest in many health applications, e.g. in neuroimaging. We propose a deep shape regression model for open planar curves that admits multimodal and high-dimensional covariates. Representing curves as complex-valued functions, we show that the conditional full Procrustes mean is the leading eigenfunction of the conditional covariance. To estimate this covariance surface, we propose a novel deep conditional covariance smoother with modality-specific encoders - e.g. splines for scalar covariates and convolutional networks for images, which classical spline smoothers cannot accommodate. Our model is by construction invariant to the translation, rotation and scaling of the input curves and handles sparsely and irregularly sampled curves. We further provide an algorithm for elastic mean estimation that also removes parametrisation by iterating covariance smoothing, rotational alignment and parametrisation alignment. We illustrate the method on simulated outlines with known conditional mean and multimodal covariates, and give a first application to hippocampal outlines from the ADNI cohort, recovering covariate effects consistent with the literature. Code is available at https://github.com/mpff/dnn-shapes.

We introduce a novel mathematical framework for analyzing and generating complex tree-shaped 3D objects, such as botanical trees and plants, which deform both in their 3D geometry and branching structure. Unlike previous works, which either consider only the skeletal structure of tree-like objects or approximate their 3D geometry using branch thickness, the proposed framework accurately models both the 3D geometry of the tree branches and the way they are interconnected. In this paper, we first generalize the Square Root Normal Fields (SRNF) representation, originally proposed for the statistical analysis of genus-0 surfaces, to tree-shaped 3D objects. We then treat tree-shaped 3D objects as points on a novel Riemannian tree-shape space equipped with a novel Riemannian metric that measures the amount of surface bending and stretching, and structural changes one needs to apply to one 3D tree-shape to align it with another. This way, deformations become trajectories in this novel tree-shape space. We analyze the theoretical properties of this novel tree-shape space and the corresponding metric and develop algorithms for computing point-wise and branch-wise correspondences and geodesic paths between complex 3D trees. We finally show how to use these building blocks for (1) computing statistical summaries, \ie means and modes of variation, of collections of tree-shaped 3D objects, and (2) synthesizing novel tree-shaped 3D objects by sampling from probability distributions fitted to a population of tree-shaped 3D objects. We demonstrate the performance and utility of the proposed framework on real and synthetic plants and botanical trees and show that it significantly outperforms the state-of-the-art.

Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. However, most studies remain limited to single or patient-specific anatomies, restricting the inclusion of population-level variability required for uncertainty quantification. A key challenge is translating medical-image segmentations, which may contain artifacts, mesh defects or disjoint domains, into topologically coherent geometries suitable for multiphysics simulations. In this work, we present a semi-automatic pipeline that converts CT-based segmentations into simulation-ready cardiac meshes within a few minutes while preserving anatomical and topological consistency. Building on modern deep learning segmentation methods, the framework incorporates a template-based registration stage to regularize artifacts and enforce mesh-quality constraints. A Chamfer-distance morphing strategy deforms a high-quality template toward each segmented heart, matching individual chambers while preserving topology. The resulting meshes are watertight, isotopological, and endowed with consistent point-to-point correspondence. The pipeline is validated on 58 healthy cardiac CT scans, including all cardiac chambers and proximal vessel segments. The resulting meshes can be represented in a unified shape space, enabling the construction of a statistical shape model of the heart and major vessels. Principal Component Analysis shows that a low-dimensional latent space efficiently captures population variability, while Gaussian Mixture Modeling enables synthetic anatomy generation. Overall, the proposed framework (released open-source) provides a pathway from raw segmentations to simulation-ready cardiac geometries, enabling anatomically consistent virtual cohorts for large-scale in silico studies.

A central objective of machine learning is to identify structure and patterns in data. Advances in data acquisition have increasingly produced datasets whose observations possess rich geometric form, giving rise to shape spaces that encode variability in object geometry. Such datasets arise across a wide range of disciplines, including biology, medicine, anthropology, and computer vision, where subtle geometric differences often carry important scientific information. Traditional machine learning methods, however, are frequently ill-equipped to account for the nonlinear geometric structure underlying these data. This survey synthesizes a rapidly growing body of work on shape space analysis, which provides a mathematical and computational framework for the study of geometric data. Drawing on ideas from differential geometry, statistics, and machine learning, we organize the literature around a common analytical pipeline: shape representation and parameterization, the rigorous construction of robust geodesic metrics, statistical analysis on shape spaces, and geometry-aware learning methods. We discuss how these tools enable the characterization of shape variability, the comparison of geometric objects, and the analysis of structural trajectories across populations and time. To illustrate the breadth of the field, we highlight applications spanning multiple scales of biological organization, including studies of subcellular morphology and primate tooth evolution. Across these and many other domains, researchers face common challenges arising from complex, nonlinear, and often unaligned geometric variation. The review concludes by identifying key theoretical and computational challenges, as well as emerging opportunities driven by increasingly large and diverse geometric datasets.

Accurate segmentation and statistical shape modeling of hand anatomy have significant implications for medical diagnostics, ergonomics, and biomechanics. This study proposes an AI-assisted reconstruction pipeline for segmenting and analyzing hand anatomy from 1,271 elbow-to-hand (e2h-CT) computed tomography scans. A Pix2Pix-based conditional generative adversarial network is first employed to remove plaster cast and background artifacts from CT volumes. The cleaned scans are then processed in 3D Slicer to extract skin and bone masks, which are converted into closed-surface mesh models. Segmented bone meshes are used to construct skeletal representations, enabling implicit skinning to align all hand models into a standardized anatomical configuration. Subsequently, non-rigid registration is performed on the hand skin surfaces using the Geodesic Based Coherent Point Drift++ (GBCPD++) algorithm to establish point-wise correspondence across subjects. Principal Component Analysis (PCA) is then applied to the registered models to quantify anatomical shape variability. The Pix2Pix preprocessing stage achieved a Dice coefficient of 0.9856 and an IoU of 0.9720 on the held-out test set. Statistical modeling was performed on a subset of 90 scans in which the fingers were fully visible and anatomically separated. The resulting statistical shape distributions demonstrate strong agreement with the U.S. Army Anthropometric Survey (ANSUR II), supporting the anatomical validity of the reconstructed models. The proposed methodology demonstrates significant potential for advancing biomechanical modeling, ergonomic optimization, prosthetic design, and precision medical diagnostics.