Domain Elastic Transform (DET) is a grid‑free, probabilistic framework that jointly aligns geometry and high‑dimensional vector‑valued functions on irregular sparse manifolds, such as those found in spatial transcriptomics. By treating data as functions rather than voxelized images, DET performs unsupervised, scalable registration through sampled point alignment and displacement interpolation, guided by a joint spatial‑functional Bayesian likelihood. Evaluations on MERFISH mouse‑brain slices and Stereo‑seq mouse‑embryo atlases show DET achieving superior spatial overlap and topology compared to existing pipelines, with an accelerated variant delivering high label‑transfer accuracy.
By Osamu Hirose, Emanuele Rodola
The growing number of medical vision foundation models highlights the need for effective model selection. However, mainstream selection methods rely on exhaustive fine-tuning, which is computationally expensive.
arXiv:2609.37037v1 Announce Type: new
Abstract: High-resolution dynamic functional connectivity (DFC) can reveal rapidly evolving brain-network interactions, but short temporal windows yield noisy, o...
By Om Roy, Yashar Moshfeghi, Keith Malcolm Smith
FiberGeoText (FGT) is a vision‑language model that clusters short‑range superficial white matter streamlines from ultra‑high‑resolution diffusion MRI into population‑level groups. It jointly encodes each streamline’s 3‑D trajectory, cortical anatomical context (via text from multiple parcellation schemes), and shape, using a pretrained large language model to unify heterogeneous anatomical descriptions. Evaluations on 0.76 mm diffusion data show that FGT outperforms state‑of‑the‑art methods in cortical parcel coherence, shape consistency, cluster‑size consistency, and cross‑subject correspondence, and it generalizes well to unseen subjects, recovering 96.7 % of learned clusters.
By Yuqian Chen, R. Jarrett Rushmore, Guikun Chen, Fan Zhang, Edward Yeterian, Nikos Makris, Yogesh Rathi, Lauren J. O'Donnell
arXiv:2609.15669v1 Announce Type: cross
Abstract: Multimodal image registration is a key component of many clinical workflows, yet it remains challenging because corresponding anatomical structures o...
By Matteo Barbieri, Giammarco La Barbera, Juan Pablo De La Plata, Sabine Sarnacki, Isabelle Bloch, Pietro Gori
The paper introduces a geometry‑guided sampling operator that directs feature sampling rather than altering convolution kernels in 3D encoder‑decoder networks. By predicting local orientations and bounded step sizes, the operator samples symmetrically around each voxel, generating compact geometric and boundary cues that improve fine‑structure segmentation. Replacing stride‑1 and stride‑2 operations in a 3D U‑Net yields consistent gains on BraTS, MSD Hepatic Vessel, and TDSC‑ABUS datasets, with better boundary metrics and fewer parameters, and the operator can be integrated into other backbones without architectural changes.
By Sizhe Wang, Himashi Peiris, Zhaolin Chen
arXiv:2610.17014v1 Announce Type: cross
Abstract: Functional brain connectome represents neural connectivity as a matrix of pairwise interactions between brain regions. Generation of functional conne...
By Protyay Dey, Ayush Roy, Hyuna Cho, Won Hwa Kim, Vishnu Suresh Lokhande
Multimodal image registration is a key component of many clinical workflows, yet it remains challenging because corresponding anatomical structures often exhibit substantially different image intensit...
The paper introduces a Geometric-to-Semantic Spherical Transfer Learning framework for labeling cortical sulci on brain surfaces. It first pre‑trains a spherical encoder on ~30,000 unlabeled UK Biobank subjects using only curvature and depth, then injects sulcal fundi lines as a soft‑initialized Topological Prior Injector to bridge the geometric‑semantic gap. Experiments show the method surpasses fully supervised baselines, achieving a mean Dice score of 0.77 and delivering the largest gains on variable and tertiary sulci.
By Saeb Tounsi, Jo\"el Chavas, Pietro Gori, Vincent Frouin, Denis Rivi\`ere, Jean-Fran\c{c}ois Mangin
The paper introduces DB‑SUiT, a surface‑based diffusion bridge that translates cortical MRI to PET images directly on the cortical manifold. It employs a conditional spherical U‑shaped vision Transformer to capture multi‑scale surface features and long‑range dependencies while incorporating demographic and subcortical information. Evaluations on two dementia datasets show that the synthesized PET surfaces outperform MRI and PET volumes in automated classification and achieve high diagnostic accuracy in a blinded reader study.
By Yitong Li, Alexandra Samoylova, Fabian Bongratz, Timo Grimmer, Dennis M. Hedderich, Igor Yakushev, Christian Wachinger
arXiv:2510. 24342v2 Announce Type: replace Abstract: Prior brain-AI alignment studies are typically constrained by specific inputs and tasks, limiting their ability to capture organizational properties across models with different modalities.
By Silin Chen, Yuzhong Chen, Caiwei Wang, Zifan Wang, Junhao Wang, Zifeng Jia, Keith M Kendrick, Tuo Zhang, Lin Zhao, Dezhong Yao, Tianming Liu, Xi Jiang
The paper introduces MedPCFM‑TED, a one‑step distillation framework that uses teacher‑guided endpoint supervision and geometric matching losses to generate cranial implants from point clouds. It outperforms existing one‑step methods on the SkullBreak benchmark, remains competitive on SkullFix, and achieves a generation time of about 0.04 s per sample. The approach demonstrates that rapid, high‑quality implant generation is possible without multiple neural evaluations during inference.
By Kamil Kwarciak, Marek Wodzinski