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BrainSeg: a generalized framework for comprehensive multimodal brain tissue segmentation, parcellation, and lesion
Shijie Huang1, Zifeng Lian1, Dengqiang Jia2
1School of Biomedical Engineering & State Key Laboratory of Advanced Medical Materials and Devices, Shanghai Tech University, Shanghai, China.
NPJ Digital Medicine
|July 10, 2026
Summary
BrainSeg offers a unified framework for comprehensive brain segmentation across all ages and imaging types. This adaptable tool achieves state-of-the-art results in tissue segmentation, parcellation, and lesion labeling for neuroimaging analysis.
Area of Science:
- Neuroimaging
- Computational Neuroscience
- Medical Image Analysis
Background:
- Accurate brain segmentation is crucial for quantitative neuroimaging.
- Existing methods struggle with generalization across human lifespan and diverse imaging modalities.
- Comprehensive Brain Segmentation (CBS) involves tissue segmentation, parcellation, and lesion labeling.
Purpose of the Study:
- To introduce BrainSeg, a novel unified framework for Comprehensive Brain Segmentation (CBS).
- To develop an adaptable framework for diverse uni- and multimodal neuroimaging data.
- To ensure generalizability across the entire human lifespan without retraining.
Main Methods:
- Utilized large-scale datasets spanning 14 gestational weeks to 100 years (45,998 scans, 26 datasets).
- Employed a proposed synthesis strategy for data augmentation.
- Developed a unified framework adaptable to diverse input scenarios.
Main Results:
- Achieved state-of-the-art performance in tissue segmentation, brain parcellation, and lesion labeling.
- Internal validation showed averaged Dice ratios up to 96.94% (tissue), 94.25% (parcellation), and 91.06% (lesion).
- External validation demonstrated high accuracy with averaged Dice ratios of 94.01% (tissue) and 91.20% (parcellation).
Conclusions:
- BrainSeg demonstrates robustness and generalizability across diverse neuroimaging conditions.
- The framework provides flexible and reliable analysis for large-scale neuroimaging studies.
- BrainSeg serves as a versatile foundational tool for quantitative neuroimaging.
