Sebastian Nørgaard Llambias, Julia Machnio, Asbjørn Munk et al.
Medical image analysis using deep learning frameworks has advanced healthcare by automating complex tasks, but many existing frameworks lack flexibility, modularity, and user-friendliness. To address these challenges, we introduce Yucca, an open-source AI framework available at https://github.com/Sllambias/yucca, designed specifically for medical imaging applications and built on PyTorch and PyTorch Lightning. Yucca features a three-tiered architecture: Functional, Modules, and Pipeline, providing a comprehensive and customizable solution. Evaluated across diverse tasks such as cerebral microbleeds detection, white matter hyperintensity segmentation, and hippocampus segmentation, Yucca achieves state-of-the-art results, demonstrating its robustness and versatility. Yucca offers a powerful, flexible, and user-friendly platform for medical image analysis, inviting community contributions to advance its capabilities and impact.
Asbjørn Munk, Stefano Cerri, Vardan Nersesjan et al.
Clinical deployment of automated brain MRI analysis faces a fundamental challenge: clinical data is heterogeneous and noisy, and high-quality labels are prohibitively costly to obtain. Self-supervised learning (SSL) can address this by leveraging the vast amounts of unlabeled data produced in clinical workflows to train robust \textit{foundation models} that adapt out-of-domain with minimal supervision. However, the development of foundation models for brain MRI has been limited by small pretraining datasets and in-domain benchmarking focused on high-quality, research-grade data. To address this gap, we organized the FOMO25 challenge as a satellite event at MICCAI 2025. FOMO25 provided participants with a large pretraining dataset, FOMO60K, and evaluated models on data sourced directly from clinical workflows in few-shot and out-of-domain settings. Tasks covered infarct classification, meningioma segmentation, and brain age regression, and considered both models trained on FOMO60K (method track) and any data (open track). Nineteen foundation models from sixteen teams were evaluated using a standardized containerized pipeline. Results show that (a) self-supervised pretraining improves generalization on clinical data under domain shift, with the strongest models trained \textit{out-of-domain} surpassing supervised baselines trained \textit{in-domain}. (b) No single pretraining objective benefits all tasks: MAE favors segmentation, hybrid reconstruction-contrastive objectives favor classification, and (c) strong performance was achieved by small pretrained models, and improvements from scaling model size and training duration did not yield reliable benefits.
Julia Machnio, Mads Nielsen, Mostafa Mehdipour Ghazi
Active learning (AL) seeks to reduce annotation costs by selecting the most informative samples for labeling, making it particularly valuable in resource-constrained settings. However, traditional evaluation methods, which focus solely on final accuracy, fail to capture the full dynamics of the learning process. To address this gap, we propose PALM (Performance Analysis of Active Learning Models), a unified and interpretable mathematical model that characterizes AL trajectories through four key parameters: achievable accuracy, coverage efficiency, early-stage performance, and scalability. PALM provides a predictive description of AL behavior from partial observations, enabling the estimation of future performance and facilitating principled comparisons across different strategies. We validate PALM through extensive experiments on CIFAR-10/100 and ImageNet-50/100/200, covering a wide range of AL methods and self-supervised embeddings. Our results demonstrate that PALM generalizes effectively across datasets, budgets, and strategies, accurately predicting full learning curves from limited labeled data. Importantly, PALM reveals crucial insights into learning efficiency, data space coverage, and the scalability of AL methods. By enabling the selection of cost-effective strategies and predicting performance under tight budget constraints, PALM lays the basis for more systematic, reproducible, and data-efficient evaluation of AL in both research and real-world applications. The code is available at: https://github.com/juliamachnio/PALM.
Julia Machnio, Mads Nielsen, Mostafa Mehdipour Ghazi
Active learning (AL) performance is known to be budget-dependent, yet regimes are typically defined by heuristic label counts that fail to generalize across datasets or architectures. We characterize AL dynamics by reframing budget regimes as shifts in the dominant generalization mechanism. By reinterpreting PAC-style risk components as dynamic interacting terms, we prove that dominance shifts are structurally unavoidable, creating a moving bottleneck for generalization. We operationalize this using measurable proxies and a segmented regression procedure to identify a tripartite taxonomy: data-driven, transition, and model-driven phases. Our framework explains the long-standing observation that representativeness, coverage, and uncertainty strategies excel at different stages. Experiments across natural and medical imaging show that AL efficiency depends on the alignment between the strategy's inductive bias and the active bottleneck. Moreover, self-supervised representation shift transitions earlier along the labeling trajectory, highlighting the role of representation quality in shaping AL dynamics. Overall, this work provides a unified framework for the next generation of transition-aware AL algorithms.
Asbjørn Munk, Stefano Cerri, Jakob Ambsdorf et al.
We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.
Nancy R. Newlin, Kurt Schilling, Serge Koudoro et al.
White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.
Julia Machnio, Sebastian Nørgaard Llambias, Mads Nielsen et al.
White matter hyperintensities (WMH) are radiological markers of small vessel disease and neurodegeneration, whose accurate segmentation and spatial localization are crucial for diagnosis and monitoring. While multimodal MRI offers complementary contrasts for detecting and contextualizing WM lesions, existing approaches often lack flexibility in handling missing modalities and fail to integrate anatomical localization efficiently. We propose a deep learning framework for WM lesion segmentation and localization that operates directly in native space using single- and multi-modal MRI inputs. Our study evaluates four input configurations: FLAIR-only, T1-only, concatenated FLAIR and T1, and a modality-interchangeable setup. It further introduces a multi-task model for jointly predicting lesion and anatomical region masks to estimate region-wise lesion burden. Experiments conducted on the MICCAI WMH Segmentation Challenge dataset demonstrate that multimodal input significantly improves the segmentation performance, outperforming unimodal models. While the modality-interchangeable setting trades accuracy for robustness, it enables inference in cases with missing modalities. Joint lesion-region segmentation using multi-task learning was less effective than separate models, suggesting representational conflict between tasks. Our findings highlight the utility of multimodal fusion for accurate and robust WMH analysis, and the potential of joint modeling for integrated predictions.