arXiv subjects

Julius C. Holzschuh

Publications and source records attributed to Julius C. Holzschuh.

4 recordsLinked to original sources

arXiv2026

nnFoundation: 3D Foundation Models for Radiology

Radiological artificial intelligence has advanced rapidly, yet most systems remain narrowly task-specific, data-intensive, and fragile under domain shift. Foundation models promise more transferable and data-efficient solutions, but existing approaches are limited in scale, evaluated narrowly, and often assume that a single pretrained model can support diverse downstream tasks. Here we present nnFoundation, complementary convolutional and transformer-based 3D radiological foundation models. Developed within the Human Radiome Project (THRP), nnFoundation is trained on 2.1 million CT, MRI, and PET image volumes from 125 institutional and public datasets. We evaluate them across 108 tasks spanning segmentation, detection, classification, report generation, and image retrieval, including evaluations under domain shift, by external partners and in low-data and low-compute regimes. Across all task types, our convolution- and transformer-based nnFoundation models consistently outperform both prior 3D foundation models and training from scratch, establishing state-of-the-art performance for radiological imaging. However, performance follows a consistent task-dependent structure: the convolutional nnFoundation model dominates spatially localized tasks, whereas the transformer-based nnFoundation model excels in tasks requiring global semantic reasoning and in frozen-feature settings. Dynamically aligning the foundation model topology with the dataset characteristics post-hoc further improves transfer across heterogeneous 3D settings. These results show that transferable 3D radiological performance is governed not by a single universal model, but by the interplay of scalable pretraining, complementary architectures, and dataset-aware adaptation. We release nnFoundation models integrated into nnU-Net and nnDetection, enabling immediate application across established radiology workflows.

cs.CV↗

arXiv2026

The TopCoW Challenge -- Topology-Aware Circle of Willis Segmentation for CT and MR Angiography

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to influence the risk, severity, and outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy remains a manual and time-consuming expert task. The CoW is commonly imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), yet few datasets with annotated CoW anatomy exist, and there have been no established benchmarks for comparing CoW segmentation algorithms. We organized the TopCoW benchmark challenge alongside the release of an annotated CoW dataset with 125 paired MRA and CTA scans from the same patients. Voxel-level annotations for 13 vessel components were created using virtual reality technology and verified by clinical experts. Participants submitted algorithms for CoW segmentation and variant classification, which we evaluated on internal and external test sets comprising 226 scans from over five centers. The benchmark includes voxel-level segmentation, CoW component detection, CoW variant classification, and two clinical application tasks. We received submissions from over 250 participants across six continents. Top-performing teams achieved over 90% Dice scores for CoW segmentation, over 80% F1 scores for detecting key vessel components, and over 70% balanced accuracy in CoW variant classification across nearly all test sets. The best algorithms also supported clinically relevant downstream tasks by accurately classifying fetal-type posterior cerebral arteries and localizing aneurysms in relation to CoW anatomy. This benchmark demonstrated the utility of CoW segmentation algorithms for some downstream clinical applications with explainability.

cs.CV↗

arXiv2026

Robustness of breast lesion segmentation under MRI undersampling improves with k-space-aware deep learning

Purpose: To assess whether breast lesion segmentation can be learned directly from acquired MRI k-space, and whether doing so improves robustness when data are accelerated or noisy. Materials and Methods: This retrospective study used public breast dynamic contrast-enhanced MRI (DCE-MRI) datasets with acquired and synthetic k-space, together with a within-dataset synthetic control. We compared four 3D U-Net variants: a hybrid k-space-to-image model, a native k-space model, and magnitude and complex image-space baselines. Models were evaluated under increasing undersampling and added complex Gaussian k-space noise. The primary outcome was patient-level Dice similarity coefficient under cross-validation, with the hybrid model prespecified as the main comparison against the magnitude image-space baseline. Results: At full sampling, the hybrid and image-space models performed similarly. As acceleration increased, the hybrid model retained substantially more segmentation accuracy and significantly outperformed the magnitude image-space baseline across moderate to high undersampling levels. The same pattern was observed when noise was added directly to k-space: the hybrid model degraded more slowly, whereas the image-space baseline failed under heavier noise. This advantage was reproduced in the within-dataset synthetic control. Feature analysis suggested that the k-space stage and image-space stage played complementary roles, with frequency-domain filtering concentrated before image-domain lesion localization. Conclusion: K-space-aware deep learning improves the robustness of breast lesion segmentation under MRI undersampling and k-space noise, while matching image-space methods at full sampling.

cs.CV↗

arXiv2024

Mitigating False Predictions In Unreasonable Body Regions

Despite considerable strides in developing deep learning models for 3D medical image segmentation, the challenge of effectively generalizing across diverse image distributions persists. While domain generalization is acknowledged as vital for robust application in clinical settings, the challenges stemming from training with a limited Field of View (FOV) remain unaddressed. This limitation leads to false predictions when applied to body regions beyond the FOV of the training data. In response to this problem, we propose a novel loss function that penalizes predictions in implausible body regions, applicable in both single-dataset and multi-dataset training schemes. It is realized with a Body Part Regression model that generates axial slice positional scores. Through comprehensive evaluation using a test set featuring varying FOVs, our approach demonstrates remarkable improvements in generalization capabilities. It effectively mitigates false positive tumor predictions up to 85% and significantly enhances overall segmentation performance.

eess.IV↗