Matthias Harders

Linus Kreitner, Johannes C. Paetzold, Nikolaus Rauch et al.

Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images.

Stefano Fogarollo, Gregor Laimer, Reto Bale et al.

Deformable medical image registration is an essential task in computer-assisted interventions. This problem is particularly relevant to oncological treatments, where precise image alignment is necessary for tracking tumor growth, assessing treatment response, and ensuring accurate delivery of therapies. Recent AI methods can outperform traditional techniques in accuracy and speed, yet they often produce unreliable deformations that limit their clinical adoption. In this work, we address this challenge and introduce a novel implicit registration framework that can predict accurate and reliable deformations. Our insight is to reformulate image registration as a signal reconstruction problem: we learn a kernel function that can recover the dense displacement field from sparse keypoint correspondences. We integrate our method in a novel hierarchical architecture, and estimate the displacement field in a coarse-to-fine manner. Our formulation also allows for efficient refinement at test time, permitting clinicians to easily adjust registrations when needed. We validate our method on challenging intra-patient thoracic and abdominal zero-shot registration tasks, using public and internal datasets from the local University Hospital. Our method not only shows competitive accuracy to state-of-the-art approaches, but also bridges the generalization gap between implicit and explicit registration techniques. In particular, our method generates deformations that better preserve anatomical relationships and matches the performance of specialized commercial systems, underscoring its potential for clinical adoption.

Johannes Sappl, Laurent Seiler, Matthias Harders et al.

Solving systems of linear equations is a problem occuring frequently in water engineering applications. Usually the size of the problem is too large to be solved via direct factorization. One can resort to iterative approaches, in particular the conjugate gradients method if the matrix is symmetric positive definite. Preconditioners further enhance the rate of convergence but hitherto only handcrafted ones requiring expert knowledge have been used. We propose an innovative approach employing Machine Learning, in particular a Convolutional Neural Network, to unassistedly design preconditioning matrices specifically for the problem at hand. Based on an in-depth case study in fluid simulation we are able to show that our learned preconditioner is able to improve the convergence rate even beyond well established methods like incomplete Cholesky factorization or Algebraic MultiGrid.