Rami Al-Maskari

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.

Ying Chen, Rami Al-Maskari, Izabela Horvath et al.

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.