Christoph Karg

Rajalakshmi Palaniappan, Christoph Karg, Nemesio Navarro-Arambula et al.

Blood vessel segmentation and -tracing are essential tasks in many medical imaging applications. Although numerous methods exist, the prevailing segment-then-fix paradigm is fundamentally limited regarding its suitability for modeling the task of complete and topologically accurate vascular network reconstruction. Here, we propose an approach to extract topologically more accurate vascular graphs from 3D image data, building upon highly successful ideas from the related biomedical tasks of cell segmentation and -tracking. Our approach first predicts voxel-wise vessel direction vectors joint with standard vessel segmentation masks. Second, to extract the vascular graph from these predictions, we introduce a direction-vector-guided extension of the TEASAR algorithm. Our approach achieves state-of-the-art performance on three benchmark datasets, spanning both synthetic and real imagery. We further demonstrate the applicability of our approach to challenging 3D micro-CT scans of rat heart vasculature. Finally, we propose meaningful and interpretable measures of topological error, namely false splits and false merges for graphs. Overall, our approach substantially improves the topological accuracy of reconstructed vascular graphs, being able to separate closely apposed vessel segments and handle multiple vascular trees within a single volume.

Jannik Franzen, Claudia Winklmayr, Vanessa E. Guarino et al.

Uncertainty Quantification (UQ) is crucial for reliable image segmentation. Yet, while the field sees continual development of novel methods, a lack of agreed-upon benchmarks limits their systematic comparison and evaluation: Current UQ methods are typically tested either on overly simplistic toy datasets or on complex real-world datasets that do not allow to discern true uncertainty. To unify both controllability and complexity, we introduce Arctique, a procedurally generated dataset modeled after histopathological colon images. We chose histopathological images for two reasons: 1) their complexity in terms of intricate object structures and highly variable appearance, which yields challenging segmentation problems, and 2) their broad prevalence for medical diagnosis and respective relevance of high-quality UQ. To generate Arctique, we established a Blender-based framework for 3D scene creation with intrinsic noise manipulation. Arctique contains 50,000 rendered images with precise masks as well as noisy label simulations. We show that by independently controlling the uncertainty in both images and labels, we can effectively study the performance of several commonly used UQ methods. Hence, Arctique serves as a critical resource for benchmarking and advancing UQ techniques and other methodologies in complex, multi-object environments, bridging the gap between realism and controllability. All code is publicly available, allowing re-creation and controlled manipulations of our shipped images as well as creation and rendering of new scenes.

Vanessa Emanuela Guarino, Claudia Winklmayr, Jannik Franzen et al.

Uncertainty Quantification (UQ) is crucial for ensuring the reliability of automated image segmentations in safety-critical domains like biomedical image analysis or autonomous driving. In segmentation, UQ generates pixel-wise uncertainty scores that must be aggregated into image-level scores for downstream tasks like Out-of-Distribution (OoD) or failure detection. Despite routine use of aggregation strategies, their properties and impact on downstream task performance have not yet been comprehensively studied. Global Average is the default choice, yet it does not account for spatial and structural features of segmentation uncertainty. Alternatives like patch-, class- and threshold-based strategies exist, but lack systematic comparison, leading to inconsistent reporting and unclear best practices. We address this gap by (1) formally analyzing properties, limitations, and pitfalls of common strategies; (2) proposing novel strategies that incorporate spatial uncertainty structure and (3) benchmarking their performance on OoD and failure detection across ten datasets that vary in image geometry and structure. We find that aggregators leveraging spatial structure yield stronger performance in both downstream tasks studied. However, the performance of individual aggregators depends heavily on dataset characteristics, so we (4) propose a meta-aggregator that integrates multiple aggregators and performs robustly across datasets.

Christoph Karg, Sebastian Stricker, Lisa Hutschenreiter et al.

In this work we present a novel approach for unsupervised multi-graph matching, which applies to problems for which a Gaussian distribution of keypoint features can be assumed. We leverage cycle consistency as loss for self-supervised learning, and determine Gaussian parameters through Bayesian Optimization, yielding a highly efficient approach that scales to large datasets. Our fully unsupervised approach enables us to reach the accuracy of state-of-the-art supervised methodology for the biomedical use case of semantic cell annotation in 3D microscopy images of the worm C. elegans. To this end, our approach yields the first unsupervised atlas of C. elegans, i.e. a model of the joint distribution of all of its cell nuclei, without the need for any ground truth cell annotation. This advancement enables highly efficient semantic annotation of cells in large microscopy datasets, overcoming a current key bottleneck. Beyond C. elegans, our approach offers fully unsupervised construction of cell-level atlases for any model organism with a stereotyped body plan down to the level of unique semantic cell labels, and thus bears the potential to catalyze respective biomedical studies in a range of further species.