TopBrain Challenge Data Release

1. Overview The TopBrain Segmentation Challenge for Whole Brain Vessel Anatomy introduces a dataset with voxel-level annotations of over 40 landmark brain vessel anatomies, encompassing both arteries and veins across magnetic resonance angiography (MRA) and computed tomography angiography (CTA) modalities. The annotation protocol proposed by TopBrain aims to unify and standardize brain vessel anatomy segmentation that can handle real-world anatomical variations. The segmentation model developed will have important research and clinical applications for all major vessels of the brain. 2. Data Usage License Following the definitions of "https://opendata.swiss/en/terms-of-use" on open data use,the following license is chosen: "Terms of data use: Open use. Must provide the source. Use for commercial purposes requires permission of the data owner. * You may use this dataset for non-commercial purposes. * You may use this dataset for commercial purposes, but you must seek prior permission from the data owner. * You must provide the source (author, title and link to the dataset)." By downloading the data, you agree with the license terms. For more information, please refer to the "License.txt" file in the same release folder. 3. Contents of Data The training data consist of 50 (=25 pairs) CTA and MRA from the TopCoW image data as the batch-1 and batch-2 releases in 2025 Voxel annotations for over 40 classes of landmark brain vessel anatomies, including the Circle of Willis (CoW) labels from the TopCoW labels New in August 2026: 36-class vessel annotations for the TopAneu challenge with two added infraclinoid classes The training (Tr) data folder has the following sub-folders: imagesTr_topbrain: Angiographic scans in nifti format, 16-bit signed. LPS+ orientation The nifti filenames are saved with schema: topcow_{modality}_{pat_id}_0000.nii.gz modality: mr for MRA, ct for CTA pat_id: patient ID, 001, 002,... labelsTr_topbrain_v1_{ct|mr}: Multiclass segmentation masks with the 2025 v1 TopBrain vessel anatomy labels Labels 1-12 and 15 are retained from TopCoW annotations TopCoW labels are a subset of TopBrain CTA has 40 labels MRA has 42 labels CTA and MRA share 34 overlapping labels labelsTr_topbrain_v2_topaneu36class: V2 multiclass segmentation masks compatible with the TopAneu challenge Added two infraclinoid classes (left and right C1-C5 vs C6-C7 for ICA) Labels 1-34 retained from TopBrain v1 labels; in total 36 classes Unified labels for both modalities (modality agnostic) Used to train the model to generate the silver-standard vessel masks for TopAneu challenge labelmap_jsons: Label-map json files with values for each anatomy class 4. Citation If you use the TopBrain challenge data in your work, please cite the TopBrain preprint and the TopCoW challenge paper: Yang K, Shi P, Huang H, Musio F, Baazaoui H, Aydin OU, Hilbert A, Hamadache RE, Yalcin C, Zhang M, Falcetta D. TopBrain segmentation challenge for whole brain vessel anatomy. medRxiv. 2026 May 30:2026-05. [Link] Yang K, Musio F, Ma Y, Juchler N, Paetzold JC, Al-Maskari R, Höher L, Li HB, Hamamci IE, Sekuboyina A, Shit S. The TopCoW Challenge—Topology-Aware Circle of Willis Segmentation for CT and MR Angiography. NEJM AI. 2026 Jul 23;3(8):AIdbp2500994. [Link] 5. Challenge Docker Submissions We also release the podium-finish Docker images from the TopBrain challenge, available at this Zenodo record: Best Performing TopBrain Segmentation Dockers https://zenodo.org/records/21959166 6. Contact Kaiyuan Yang ([e-mail]) from University of ZurichPengcheng Shi ([e-mail]) from Medical Image Insights ---Updated August-17-2026