Nico Disch

Saikat Roy, Tassilo Wald, Gregor Koehler et al.

Foundation models have taken over natural language processing and image generation domains due to the flexibility of prompting. With the recent introduction of the Segment Anything Model (SAM), this prompt-driven paradigm has entered image segmentation with a hitherto unexplored abundance of capabilities. The purpose of this paper is to conduct an initial evaluation of the out-of-the-box zero-shot capabilities of SAM for medical image segmentation, by evaluating its performance on an abdominal CT organ segmentation task, via point or bounding box based prompting. We show that SAM generalizes well to CT data, making it a potential catalyst for the advancement of semi-automatic segmentation tools for clinicians. We believe that this foundation model, while not reaching state-of-the-art segmentation performance in our investigations, can serve as a highly potent starting point for further adaptations of such models to the intricacies of the medical domain. Keywords: medical image segmentation, SAM, foundation models, zero-shot learning

Kaiyuan Yang, Fabio Musio, Yihui Ma et al.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building.

Marcello Longo, Joost A. A. Opschoor, Nico Disch et al.

On general regular simplicial partitions $\mathcal{T}$ of bounded polytopal domains $Ω\subset \mathbb{R}^d$, $d\in\{2,3\}$, we construct \emph{exact neural network (NN) emulations} of all lowest order finite element spaces in the discrete de Rham complex. These include the spaces of piecewise constant functions, continuous piecewise linear (CPwL) functions, the classical ``Raviart-Thomas element'', and the ``Nédélec edge element''. For all but the CPwL case, our network architectures employ both ReLU (rectified linear unit) and BiSU (binary step unit) activations to capture discontinuities. In the important case of CPwL functions, we prove that it suffices to work with pure ReLU nets. Our construction and DNN architecture generalizes previous results in that no geometric restrictions on the regular simplicial partitions $\mathcal{T}$ of $Ω$ are required for DNN emulation. In addition, for CPwL functions our DNN construction is valid in any dimension $d\geq 2$. Our ``FE-Nets'' are required in the variationally correct, structure-preserving approximation of boundary value problems of electromagnetism in nonconvex polyhedra $Ω\subset \mathbb{R}^3$. They are thus an essential ingredient in the application of e.g., the methodology of ``physics-informed NNs'' or ``deep Ritz methods'' to electromagnetic field simulation via deep learning techniques. We indicate generalizations of our constructions to higher-order compatible spaces and other, non-compatible classes of discretizations, in particular the ``Crouzeix-Raviart'' elements and Hybridized, Higher Order (HHO) methods.