Organizations: Murdoch University, WA, Australia. · University of Western Australia, WA, Australia. · Johns Hopkins University, USA.
Abstract
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.
Compositional data -- vectors encoding relative proportions -- arise across scientific domains, including ecology, geochemistry, and genomics. The features in these data often come with known hierarchical structure (e.g., taxonomies, phylogenies, ontologies), yet existing methods either ignore this structure, discard the intrinsic Aitchison geometry, are designed for binary trees, or yield incomplete coordinate systems. We describe PolyILR, a canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology. Our construction defines a weighted local geometry at each internal node capturing full branching structure, then lifts these to a global orthonormal basis where every coordinate corresponds to a specific tree location. On microbiome and single-cell benchmarks, PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution. We also establish a novel theoretical connection to softmax classifiers, suggesting possible applications to probabilistic modeling.
Accurate 3D plant organ segmentation is fundamental to automated phenotyping. Existing approaches rely on annotated training data or species-specific model configurations. We present an annotation-free pipeline for 3D plant organ segmentation, combining text-prompted SAM3 segmentation with semantic neural radiance fields (NeRFs). Given only multi-view RGB images and a list of class names, our zero-shot pipeline produces semantically labeled 3D point clouds without manual annotation, per-species fine-tuning, or domain-specific preprocessing. Multi-view NeRF fusion acts as effective implicit consensus mechanism that lifts imperfect per-frame masks into accurate 3D labels. On a controlled Begonia maculata testbed the SAM3 pipeline achieves 92.6% mIoU, reaching 95.9% of the oracle upper bound established with perfect ground-truth masks. The pipeline was further evaluated on a new dataset spanning ten diverse plant point clouds reaching an average 0.856 mIoU, with leaf and pot IoU above 0.91 and 0.90 for every species, respectively. These results demonstrate that annotation-free 3D plant organ segmentation is now feasible and approaching the range of supervised methods.
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.
Gary P. T. Choi, Khanh Dao Duc, Shira Faigenbaum-Golovin +6