TopBrain 🔝🧠 Segmentation Challenge for Whole Brain Vessel Anatomy¶
Segment over 40 landmark brain vessel anatomies for both CTA and MRA!¶
🐰 News:
[09-15] Contact form for MICCAI event 🇰🇷
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👉 Please fill up this contact form by Sep 21
https://forms.office.com/e/hZWnnZKNkd
so we can contact you for the event planning.
[09-15] Final Test phases are now open for submission! (Only one submission per team for each phase!)
- 🏆 Submit to final test phases:
Sep 15 - Sep 21, 2025
- 🚨 New change by GC: Submissions to multiple phases in a challenge cannot happen in parallel! This means you have to allocate at least 1.5 hours between your MRA and CTA submissions, since they are now blocking each other.
- Submit to Final Test CTA Segmentation
- Submit to Final Test MRA Segmentation
Sep 15 - Sep 21, 2025- Submit to Final Test CTA Segmentation
- Submit to Final Test MRA Segmentation
[09-09] Validation phases are now open for submission! (To validate your docker technically, not counted towards the ranking.)
- 🧸 Submit to validation phases:
Sep 09 - Sep 21, 2025
- Submit to Validation CTA Segmentation
- Submit to Validation MRA Segmentation
Sep 09 - Sep 21, 2025- Submit to Validation CTA Segmentation
- Submit to Validation MRA Segmentation
[09-07] 🐋 Template for algorithm submission is now on GitHub! Check it out: 👉 🔗 TopBrain_Algo_Submission
[08-14] 💽 Batch-2 of TopBrain training data is now available on Zenodo! Check it out: 👉 🔗 Access TopBrain data on Zenodo
From the team behind the TopCoW 🐮 challenge, we present a new challenge called TopBrain 🔝🧠 to segment the whole brain vessel anatomy! Previously, TopCoW focused on the the vessels from the Circle of Willis (CoW). Now TopBrain will extend upon CoW to cover all the major landmark arteries and veins of a brain angiogram!
Why TopBrain?¶
- First dataset with voxel annotations on over 40 landmark brain vessel anatomies
- for both major arteries and veins
- for both most common non-invasive angiography modalities
- magnetic resonance angiography (MRA)
- and computed tomography angiography (CTA)
- Unify anatomy literature and standardize anatomy atlas for brain vessel segmentation
- consolidates brain vessel anatomy knowledge
- annotation protocol proposed by TopBrain aims to address real-world anatomical variations
- Landmark vessel anatomy serves as an anchor point for downstream tasks
- labeled 40+ landmark vessels are highly clinically relevant
- Tailored metrics for whole brain vessel segmentation
The segmentation model developed will have important research and clinical applications for all major vessels of the brain.
1 Task, 2 Tracks, 40+ Vessels¶
TopBrain has 1 multiclass segmentation task for 2 modality tracks, namely CTA and MRA tracks. The input is single-modality. The task is to segment 40+ vessel classes on a CTA or MRA scan.
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
- 👉 Go to our Data page to find out more!
Metrics¶
- Focused on the topology of segmentation
- centerline, connected components, and neighbourhood
- minimize topological mistakes in connectivity, fragmentation, and crossover
- suited for whole brain vessel context
- 👉 Check out our Assessment page for more info!
Participation Rules¶
- Participants may use additional data provided that they disclose the data and usage in their algorithm description
- Top 3 teams will get a booklet "Anatomy of the Brain Illustrated Pocket Anatomy" 🧠 and a Swiss wooden cow toy 🐄 as souverniors :)
- 👉 More info is on our Rules page
Timeline 🗓️¶
- ⏳ Post-MICCAI play-off phase: tentatively early Dec 2025
- ⏳ Post-MICCAI batch-3 release of training data: tentatively mid Nov 2025
- ✅ MICCAI challenge event milestone:
Sep 23, 2025- joint program with the 🤝 SWITCH Workshop
- ✅ Submit to final-test phase
Sep 15 - Sep 21, 2025 - ✅ Submit to validation phase
Sep 09 - Sep 21, 2025 - ✅ Release of batch-2 of training data:
August 14, 2025 - ✅ Release of batch-1 of training data:
July 30, 2025
Links¶
TopCoW Challenge
Check out the 👉 📰 summary paper of our previous TopCoW challenge! You can find out more about the data used and lessons we learned on CoW multiclass segmentation, which may be useful for solving the more complex TopBrain task:
- Yang, Musio, Ma, et al. "Benchmarking the CoW with the TopCoW challenge: Topology-aware anatomical segmentation of the Circle of Willis for CTA and MRA." ArXiv (2025): arXiv-2312. [Link]
Our GitHub
Please visit our GitHub for repos and documentations on:
Forum
We have a forum to post your questions! 👉 Forum link