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Domain Elastic Transform: Bayesian Function Registration for High-Dimensional Scientific Data

Hirose, Osamu, Rodola, Emanuele

arXiv.org Machine Learning

Nonrigid registration is conventionally divided into point set registration, which aligns sparse geometries, and image registration, which aligns continuous intensity fields on regular grids. However, this dichotomy creates a critical bottleneck for emerging scientific data, such as spatial transcriptomics, where high-dimensional vector-valued functions, e.g., gene expression, are defined on irregular, sparse manifolds. Consequently, researchers currently face a forced choice: either sacrifice single-cell resolution via voxelization to utilize image-based tools, or ignore the critical functional signal to utilize geometric tools. To resolve this dilemma, we propose Domain Elastic Transform (DET), a grid-free probabilistic framework that unifies geometric and functional alignment. By treating data as functions on irregular domains, DET registers high-dimensional signals directly without binning. We formulate the problem within a rigorous Bayesian framework, modeling domain deformation as an elastic motion guided by a joint spatial-functional likelihood. The method is fully unsupervised and scalable, utilizing feature-sensitive downsampling to handle massive atlases. We demonstrate that DET achieves 92\% topological preservation on MERFISH data where state-of-the-art optimal transport methods struggle ($<$5\%), and successfully registers whole-embryo Stereo-seq atlases across developmental stages -- a task involving massive scale and complex nonrigid growth. The implementation of DET is available on {https://github.com/ohirose/bcpd} (since Mar, 2025).


Unsupervised learning of object frames by dense equivariant image labelling

Neural Information Processing Systems

One of the key challenges of visual perception is to extract abstract models of 3D objects and object categories from visual measurements, which are affected by complex nuisance factors such as viewpoint, occlusion, motion, and deformations. Starting from the recent idea of viewpoint factorization, we propose a new approach that, given a large number of images of an object and no other supervision, can extract a dense object-centric coordinate frame. This coordinate frame is invariant to deformations of the images and comes with a dense equivariant labelling neural network that can map image pixels to their corresponding object coordinates. We demonstrate the applicability of this method to simple articulated objects and deformable objects such as human faces, learning embeddings from random synthetic transformations or optical flow correspondences, all without any manual supervision.


Learning Conditional Deformable Templates with Convolutional Networks

Adrian Dalca, Marianne Rakic, John Guttag, Mert Sabuncu

Neural Information Processing Systems

In these frameworks, templates are constructed using an iterative process of template estimation and alignment, which is often computationally very expensive. Due in part to this shortcoming, most methods compute asingle template for the entire population of images, or a few templates for specific sub-groups of the data.