Segmentation¶
BraTS Orchestrator provides top-performing segmentation algorithms from multiple BraTS challenges.
Adult Glioma (Pre & Post-Treatment)¶
Segmentation on pre- and post-treatment brain MRI exams (4 modalities: T1c, T1n, T2f, T2w).
from brats import AdultGliomaPreAndPostTreatmentSegmenter
from brats.constants import AdultGliomaPreAndPostTreatmentAlgorithms
segmenter = AdultGliomaPreAndPostTreatmentSegmenter(
algorithm=AdultGliomaPreAndPostTreatmentAlgorithms.BraTS25_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Ishika Jain, et al. | N/A |  |
BraTS25_1 |
| 2025 | 2nd | Qu Lin, et al. | N/A |  |
BraTS25_2 |
| 2025 | 3rd | Liwei Jin, et al. | N/A | |
BraTS25_3A |
| 2025 | 3rd | Adrian Celaya, et al. | N/A | |
BraTS25_3B |
| 2024 | 1st | André Ferreira, et al. | Link | |
BraTS24_1 |
| 2024 | 2nd | Heejong Kim, et al. | Link | |
BraTS24_2 |
| 2024 | 3rd | Adrian Celaya | N/A | |
BraTS24_3 |
Atlas: MNI152 atlas (Zenodo). Companion: GlioMODA.
Adult Glioma (Pre-Treatment)¶
Pre-treatment glioma segmentation (4 modalities).
from brats import AdultGliomaPreTreatmentSegmenter
from brats.constants import AdultGliomaPreTreatmentAlgorithms
segmenter = AdultGliomaPreTreatmentSegmenter(
algorithm=AdultGliomaPreTreatmentAlgorithms.BraTS23_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2023 | 1st | André Ferreira, et al. | Link | |
BraTS23_1 |
| 2023 | 2nd | Andriy Myronenko, et al. | Link | |
BraTS23_2 |
| 2023 | 3rd | Fadillah Adamsyah Maani, et al. | Link | |
BraTS23_3 |
Atlas: SRI24 atlas (Zenodo). Companion: GlioMODA.
BraTS-Africa¶
Glioma segmentation on Sub-Saharan African patient population MRI exams (4 modalities).
from brats import AfricaSegmenter
from brats.constants import AfricaAlgorithms
segmenter = AfricaSegmenter(
algorithm=AfricaAlgorithms.BraTS25_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Claudia Takyi Ankomah, et al. | N/A | |
BraTS25_1 |
| 2025 | 2nd | William Boonzaier, et al. | N/A | |
BraTS25_2A |
| 2025 | 2nd | Mohtady Barakat, et al. | N/A | |
BraTS25_2B |
| 2025 | 3rd | Ahmed Jaheen, et al. | N/A | |
BraTS25_3 |
| 2024 | 1st | Abhijeet Parida, et al. | Link | |
BraTS24_1 |
| 2024 | 2nd | Yanguang Zhao, et al. | Link | |
BraTS24_2 |
| 2024 | 3rd | Sarim Hashmi, et al. | Link | |
BraTS24_3 |
| 2023 | 1st | Andriy Myronenko, et al. | Link | |
BraTS23_1 |
| 2023 | 2nd | Alyssa R Amod, et al. | Link | |
BraTS23_2 |
| 2023 | 3rd | Ziyan Huang, et al. | Link | |
BraTS23_3 |
Atlas: SRI24 atlas (Zenodo).
Meningioma¶
Meningioma segmentation on brain MRI exams (4 modalities).
from brats import MeningiomaSegmenter
from brats.constants import MeningiomaAlgorithms
segmenter = MeningiomaSegmenter(
algorithm=MeningiomaAlgorithms.BraTS25_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Yu Haitao, et al. | N/A | |
BraTS25_1 |
| 2025 | 2nd | Mohammad Mahdi Danesh Pajouh, et al. | N/A | |
BraTS25_2 |
| 2023 | 1st | Andriy Myronenko, et al. | Link | |
BraTS23_1 |
| 2023 | 2nd | Ziyan Huang, et al. | Link | |
BraTS23_2 |
| 2023 | 3rd | Daniel Capellán-Martín et al. | Link | |
BraTS23_3 |
Atlas: SRI24 atlas (Zenodo).
Meningioma Radio Therapy¶
Segmentation on T1c-only MRI exams.
from brats import MeningiomaRTSegmenter
from brats.constants import MeningiomaRTAlgorithms
segmenter = MeningiomaRTSegmenter(
algorithm=MeningiomaRTAlgorithms.BraTS25_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Valeria Abramova, et al. | N/A | |
BraTS25_1 |
| 2025 | 2nd | Sanskriti Srivastava, et al. | N/A | |
BraTS25_2 |
| 2025 | 3rd | Nima Sadeghzadeh, et al. | N/A | |
BraTS25_3 |
| 2024 | 1st | Valeria Abramova | N/A | |
BraTS24_1 |
| 2024 | 2nd | Mehdi Astaraki | N/A | |
BraTS24_2 |
| 2024 | 3rd | Andre Ferreira, et al. | Link | |
BraTS24_3 |
Atlas: MRI data was native space. SRI24 atlas used for pre-operative challenges.
Brain Metastases¶
Brain metastases segmentation for pre- and post-treatment cases (4 modalities).
from brats import MetastasesSegmenter
from brats.constants import MetastasesAlgorithms
segmenter = MetastasesSegmenter(
algorithm=MetastasesAlgorithms.BraTS25_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Maria Bancerek, et al. | N/A | |
BraTS25_1 |
| 2025 | 2nd | Wes Krikorian, et al. | N/A | |
BraTS25_2 |
| 2023 | 1st | Andriy Myronenko, et al. | Link | |
BraTS23_1 |
| 2023 | 2nd | Siwei Yang, et al. | Link | |
BraTS23_2 |
| 2023 | 3rd | Ziyan Huang, et al. | Link | |
BraTS23_3 |
Atlas: SRI24 atlas (Zenodo). Companion: AURORA.
Pediatric¶
Pediatric brain tumor segmentation (4 modalities).
from brats import PediatricSegmenter
from brats.constants import PediatricAlgorithms
segmenter = PediatricSegmenter(
algorithm=PediatricAlgorithms.BraTS25_1,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Yuxiao Yi, et al. | N/A | |
BraTS25_1 |
| 2025 | 2nd | Meng-Yuan Chen, et al. | N/A | |
BraTS25_2 |
| 2025 | 3rd | Haitao Yu, et al. | N/A | |
BraTS25_3 |
| 2024 | 1st | Mehdi Astaraki | N/A | |
BraTS24_1 |
| 2024 | 2nd | Tim Mulvany, et al. | Link | |
BraTS24_2 |
| 2024 | 3rd | Sarim Hashmi, et al. | Link | |
BraTS24_3 |
| 2023 | 1st | Daniel Capellán-Martín, et al. | Link | |
BraTS23_1 |
| 2023 | 2nd | Andriy Myronenko, et al. | Link | |
BraTS23_2 |
| 2023 | 3rd | Yubo Zhou | Link | |
BraTS23_3 |
Atlas: SRI24 atlas (Zenodo). Companion: PeTu.
BraTS-GoAT¶
Segmentation algorithm that adapts and generalizes to different brain tumors with varying label definitions (4 modalities).
from brats import GoATSegmenter
from brats.constants import GoATAlgorithms
segmenter = GoATSegmenter(
algorithm=GoATAlgorithms.BraTS25_1A,
cuda_devices="0",
)
segmenter.infer_single(
t1c="path/to/t1c.nii.gz",
t1n="path/to/t1n.nii.gz",
t2f="path/to/t2f.nii.gz",
t2w="path/to/t2w.nii.gz",
output_file="segmentation.nii.gz",
)
| Year | Rank | Author | Paper | CPU | Key Enum |
|---|---|---|---|---|---|
| 2025 | 1st | Meng-Yuan Chen, et al. | N/A | |
BraTS25_1A |
| 2025 | 1st | To-Liang Hsu, et al. | N/A | |
BraTS25_1B |
| 2025 | 1st | Vaidehi Satushe, et al. | N/A | |
BraTS25_1C |
| 2025 | 1st | Simone Bendazzoli, et al. | N/A | |
BraTS25_1D |
| 2024 | 1st | Frank Miao, Shengjie Niu | N/A | |
BraTS24_1 |
Atlas: Datasets adapted from other challenges; atlas type depends on original dataset.
Batch Processing¶
Process multiple subjects at once by organizing them into subdirectories:
segmenter.infer_batch(
data_folder="path/to/subjects/",
output_folder="path/to/output/",
)
Folder Structure
Each subject must be in its own subdirectory containing the required modalities. See the API reference for the expected layout.
Legacy Algorithms
Some legacy segmentation algorithms from BraTS challenges before 2023 are available via BraTS Toolkit.