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

arXiv: https://arxiv.org/abs/2312.17670 · HTML: https://mlsanity.com/paper/2312.17670/

## Key facts

- Cited by 50 papers in the map (data through 14 Oct 2026).
- Builds on 30 of its 124 references that are in the map.
- First posted on arXiv 29 Dec 2023.

## Builds on (most cited first, 30 of 30)

- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [A Style-Based Generator Architecture for Generative Adversarial Networks](https://mlsanity.com/paper/1812.04948/) (2018)
- [You Only Look Once: Unified, Real-Time Object Detection](https://mlsanity.com/paper/1506.02640/) (2015)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Video Swin Transformer](https://mlsanity.com/paper/2106.13230/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [3D MRI brain tumor segmentation using autoencoder regularization](https://mlsanity.com/paper/1810.11654/) (2018)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [Topology-Preserving Deep Image Segmentation](https://mlsanity.com/paper/1906.05404/) (2019)
- [Metrics reloaded: Recommendations for image analysis validation](https://mlsanity.com/paper/2206.01653/) (2022)
- [Boundary IoU: Improving Object-Centric Image Segmentation Evaluation](https://mlsanity.com/paper/2103.16562/) (2021)
- [MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation](https://mlsanity.com/paper/2303.09975/) (2023)
- [Automated brain extraction of multi-sequence MRI using artificial neural networks](https://mlsanity.com/paper/1901.11341/) (2019)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)
- [nnDetection: A Self-configuring Method for Medical Object Detection](https://mlsanity.com/paper/2106.00817/) (2021)
- [Understanding metric-related pitfalls in image analysis validation](https://mlsanity.com/paper/2302.01790/) (2023)
- [Learning Topological Interactions for Multi-Class Medical Image Segmentation](https://mlsanity.com/paper/2207.09654/) (2022)
- [Scalable Robust Graph and Feature Extraction for Arbitrary Vessel Networks in Large Volumetric Datasets](https://mlsanity.com/paper/2102.03444/) (2021)
- [A skeletonization algorithm for gradient-based optimization](https://mlsanity.com/paper/2309.02527/) (2023)
- [A Generalized Surface Loss for Reducing the Hausdorff Distance in Medical Imaging Segmentation](https://mlsanity.com/paper/2302.03868/) (2023)
- [Towards automated brain aneurysm detection in TOF-MRA: open data, weak labels, and anatomical knowledge](https://mlsanity.com/paper/2103.06168/) (2021)
- [Automated Intracranial Artery Labeling using a Graph Neural Network and Hierarchical Refinement](https://mlsanity.com/paper/2007.14472/) (2020)
- [NexToU: Efficient Topology-Aware U-Net for Medical Image Segmentation](https://mlsanity.com/paper/2305.15911/) (2023)
- [A2V: A Semi-Supervised Domain Adaptation Framework for Brain Vessel Segmentation via Two-Phase Training Angiography-to-Venography Translation](https://mlsanity.com/paper/2309.06075/) (2023)
- [syGlass: Interactive Exploration of Multidimensional Images Using Virtual Reality Head-mounted Displays](https://mlsanity.com/paper/1804.08197/) (2018)
- [Accurate Detection of Mediastinal Lesions with nnDetection](https://mlsanity.com/paper/2303.11214/) (2023)

## Built on by (most cited first, 30 of 50)

- [Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures](https://mlsanity.com/paper/2404.03010/) (2024)
- [nnInteractive: Redefining 3D Promptable Segmentation](https://mlsanity.com/paper/2503.08373/) (2025)
- [Centerline Boundary Dice Loss for Vascular Segmentation](https://mlsanity.com/paper/2407.01517/) (2024)
- [An OpenMind for 3D medical vision self-supervised learning](https://mlsanity.com/paper/2412.17041/) (2024)
- [vesselFM: A Foundation Model for Universal 3D Blood Vessel Segmentation](https://mlsanity.com/paper/2411.17386/) (2024)
- [Topograph: An efficient Graph-Based Framework for Strictly Topology Preserving Image Segmentation](https://mlsanity.com/paper/2411.03228/) (2024)
- [Topologically Faithful Multi-class Segmentation in Medical Images](https://mlsanity.com/paper/2403.11001/) (2024)
- [LesionLocator: Zero-Shot Universal Tumor Segmentation and Tracking in 3D Whole-Body Imaging](https://mlsanity.com/paper/2502.20985/) (2025)
- [3D Vessel Graph Generation Using Denoising Diffusion](https://mlsanity.com/paper/2407.05842/) (2024)
- [GLCP: Global-to-Local Connectivity Preservation for Tubular Structure Segmentation](https://mlsanity.com/paper/2507.21328/) (2025)
- [Pitfalls of topology-aware image segmentation](https://mlsanity.com/paper/2412.14619/) (2024)
- [VasTSD: Learning 3D Vascular Tree-state Space Diffusion Model for Angiography Synthesis](https://mlsanity.com/paper/2503.12758/) (2025)
- [Topology Optimization in Medical Image Segmentation with Fast Euler Characteristic](https://mlsanity.com/paper/2507.23763/) (2025)
- [ISLES'24: Final Infarct Prediction with Multimodal Imaging and Clinical Data. Where Do We Stand?](https://mlsanity.com/paper/2408.10966/) (2024)
- [BrainMRDiff: A Diffusion Model for Anatomically Consistent Brain MRI Synthesis](https://mlsanity.com/paper/2504.04532/) (2025)
- [Hierarchical Part-based Generative Model for Realistic 3D Blood Vessel](https://mlsanity.com/paper/2507.15223/) (2025)
- [Universal Topology Refinement for Medical Image Segmentation with Polynomial Feature Synthesis](https://mlsanity.com/paper/2409.09796/) (2024)
- [MedSAMix: A Training-Free Model Merging Approach for Medical Image Segmentation](https://mlsanity.com/paper/2508.11032/) (2025)
- [Medverse: A Universal Model for Full-Resolution 3D Medical Image Segmentation, Transformation and Enhancement](https://mlsanity.com/paper/2509.09232/) (2025)
- [ReX-MLE: The Autonomous Agent Benchmark for Medical Imaging Challenges](https://mlsanity.com/paper/2512.17838/) (2025)
- [Semantically Consistent Discrete Diffusion for 3D Biological Graph Modeling](https://mlsanity.com/paper/2507.04856/) (2025)
- [The Missing Piece: A Case for Pre-Training in 3D Medical Object Detection](https://mlsanity.com/paper/2509.15947/) (2025)
- [VesselTok: Tokenizing Vessel-like 3D Biomedical Graph Representations for Reconstruction and Generation](https://mlsanity.com/paper/2603.18797/) (2026)
- [Topology-Aware Exploration of Circle of Willis for CTA and MRA: Segmentation, Detection, and Classification](https://mlsanity.com/paper/2410.15614/) (2024)
- [Neuroverse3D: Developing In-Context Learning Universal Model for Neuroimaging in 3D](https://mlsanity.com/paper/2503.02410/) (2025)
- [TopoMortar: A dataset to evaluate image segmentation methods focused on topology accuracy](https://mlsanity.com/paper/2503.03365/) (2025)
- [Skelite: Compact Neural Networks for Efficient Iterative Skeletonization](https://mlsanity.com/paper/2503.07369/) (2025)
- [Parametric shape models for vessels learned from segmentations via differentiable voxelization](https://mlsanity.com/paper/2507.02576/) (2025)
- [Does the Skeleton-Recall Loss Really Work?](https://mlsanity.com/paper/2508.11374/) (2025)
- [TopoSculpt: Betti-Steered Topological Sculpting of 3D Fine-grained Tubular Shapes](https://mlsanity.com/paper/2509.03938/) (2025)

## Abstract (arXiv)

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.