arXiv subjects

Joel Honkamaa

Publications and source records attributed to Joel Honkamaa.

6 recordsLinked to original sources

arXiv2026

Beyond the LUMIR challenge: The pathway to foundational registration models

Medical image challenges have played a transformative role in advancing the field, catalyzing innovation and establishing new performance benchmarks. Image registration, a foundational task in neuroimaging, has similarly advanced through the Learn2Reg initiative. Building on this, we introduce the Large-scale Unsupervised Brain MRI Image Registration (LUMIR) challenge, a next-generation benchmark for unsupervised brain MRI registration. Previous challenges relied upon anatomical label maps, however LUMIR provides 4,014 unlabeled T1-weighted MRIs for training, encouraging biologically plausible deformation modeling through self-supervision. Evaluation includes 590 in-domain test subjects and extensive zero-shot tasks across disease populations, imaging protocols, and species. Deep learning methods consistently achieved state-of-the-art performance and produced anatomically plausible, diffeomorphic deformation fields. They outperformed several leading optimization-based methods and remained robust to most domain shifts. These findings highlight the growing maturity of deep learning in neuroimaging registration and its potential to serve as a foundation model for general-purpose medical image registration.

eess.IV↗

arXiv2026

Learn2Reg 2024: New Benchmark Datasets Driving Progress on New Challenges

Medical image registration is critical for clinical applications, and fair benchmarking of different methods is essential for monitoring ongoing progress in the field. To date, the Learn2Reg 2020-2023 challenges have released several complementary datasets and established metrics for evaluations. Building on this foundation, the 2024 edition expands the challenge's scope to cover a wider range of registration scenarios, particularly in terms of modality diversity and task complexity, by introducing three new tasks, including large-scale multi-modal registration and unsupervised inter-subject brain registration, as well as the first microscopy-focused benchmark within Learn2Reg. The new datasets also inspired new method developments, including invertibility constraints, pyramid features, keypoints alignment and instance optimisation. Visit Learn2Reg at https://learn2reg.grand-challenge.org.

eess.IV↗

arXiv2025

New multimodal similarity measure for image registration via modeling local functional dependence with linear combination of learned basis functions

The deformable registration of images of different modalities, essential in many medical imaging applications, remains challenging. The main challenge is developing a robust measure for image overlap despite the compared images capturing different aspects of the underlying tissue. Here, we explore similarity metrics based on functional dependence between intensity values of registered images. Although functional dependence is too restrictive on the global scale, earlier work has shown competitive performance in deformable registration when such measures are applied over small enough contexts. We confirm this finding and further develop the idea by modeling local functional dependence via the linear basis function model with the basis functions learned jointly with the deformation. The measure can be implemented via convolutions, making it efficient to compute on GPUs. We release the method as an easy-to-use tool and show good performance on three datasets compared to well-established baseline and earlier functional dependence-based methods.

cs.CV↗

arXiv2025

Strategies for Robust Deep Learning Based Deformable Registration

Deep learning based deformable registration methods have become popular in recent years. However, their ability to generalize beyond training data distribution can be poor, significantly hindering their usability. LUMIR brain registration challenge for Learn2Reg 2025 aims to advance the field by evaluating the performance of the registration on contrasts and modalities different from those included in the training set. Here we describe our submission to the challenge, which proposes a very simple idea for significantly improving robustness by transforming the images into MIND feature space before feeding them into the model. In addition, a special ensembling strategy is proposed that shows a small but consistent improvement.

cs.CV↗

arXiv2024

SITReg: Multi-resolution architecture for symmetric, inverse consistent, and topology preserving image registration

Deep learning has emerged as a strong alternative for classical iterative methods for deformable medical image registration, where the goal is to find a mapping between the coordinate systems of two images. Popular classical image registration methods enforce the useful inductive biases of symmetricity, inverse consistency, and topology preservation by construction. However, while many deep learning registration methods encourage these properties via loss functions, no earlier methods enforce all of them by construction. Here, we propose a novel registration architecture based on extracting multi-resolution feature representations which is by construction symmetric, inverse consistent, and topology preserving. We also develop an implicit layer for memory efficient inversion of the deformation fields. Our method achieves state-of-the-art registration accuracy on three datasets. The code is available at https://github.com/honkamj/SITReg.

cs.CV↗

arXiv2023

Deformation equivariant cross-modality image synthesis with paired non-aligned training data

Cross-modality image synthesis is an active research topic with multiple medical clinically relevant applications. Recently, methods allowing training with paired but misaligned data have started to emerge. However, no robust and well-performing methods applicable to a wide range of real world data sets exist. In this work, we propose a generic solution to the problem of cross-modality image synthesis with paired but non-aligned data by introducing new deformation equivariance encouraging loss functions. The method consists of joint training of an image synthesis network together with separate registration networks and allows adversarial training conditioned on the input even with misaligned data. The work lowers the bar for new clinical applications by allowing effortless training of cross-modality image synthesis networks for more difficult data sets.

cs.CV↗