diff --git a/README.md b/README.md index a201368..6126fc5 100644 --- a/README.md +++ b/README.md @@ -36,13 +36,19 @@ pip install brats - **Docker**: Installation instructions on the official [website](https://docs.docker.com/get-docker/) - **NVIDIA Container Toolkit**: Refer to the [NVIDIA install guide](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html) and the official [GitHub page](https://github.com/NVIDIA/nvidia-container-toolkit) -## Use Cases and Tutorials -A minimal example to create a segmentation could look like this: +## Available Algorithms and Usage + +### Segmentation +
+ + Adult Glioma Segmentation +
+ ```python from brats import AdultGliomaSegmenter -from brats.utils.constants import AdultGliomaAlgorithms +from brats.constants import AdultGliomaAlgorithms segmenter = AdultGliomaSegmenter(algorithm=AdultGliomaAlgorithms.BraTS23_1, cuda_devices="0") # these parameters are optional, by default the winning algorithm will be used on cuda:0 @@ -55,19 +61,10 @@ segmenter.infer_single( ) ``` -For more examples and details please refer to our extensive Notebook tutorials here [NBViewer](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/BraTS/tutorial.ipynb) ([GitHub](https://github.com/BrainLesion/tutorials/blob/main/BraTS/tutorial.ipynb)). For the best experience open the notebook in Colab. - -## Algorithms - -
- - Adult Glioma Segmentation -
- **Class:** `brats.AdultGliomaSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.AdultGliomaSegmenter)) -| Year | Rank | Author | Paper | CPU Support | Key Enum | -| ---- | ---- | --------------------------------- | ------------------------------------------ | ----------- | ------------------------------------------------------------------------------------------------------------------------ | +| Year | Rank | Author | Paper | CPU Support | Key Enum | +| ---- | ---- | --------------------------------- | ------------------------------------------ | ----------- | -------------------------------------------------------------------------------------------------------------------------- | | 2023 | 1st | _André Ferreira, et al._ | [Link](https://arxiv.org/abs/2402.17317v1) | ❌ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_1) | | 2023 | 2nd | _Andriy Myronenko, et al._ | N/A | ❌ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_2) | | 2023 | 3rd | _Fadillah Adamsyah Maani, et al._ | N/A | ❌ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_3) | @@ -78,10 +75,25 @@ For more examples and details please refer to our extensive Notebook tutorials h BraTS-Africa Segmentation
+```python +from brats import AfricaSegmenter +from brats.constants import AfricaAlgorithms + +segmenter = AfricaSegmenter(algorithm=AfricaAlgorithms.BraTS23_1, cuda_devices="0") +# these parameters are optional, by default the winning algorithm will be used on cuda: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", +) +``` + **Class:** `brats.AfricaSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.AfricaSegmenter)) -| Year | Rank | Author | Paper | CPU Support | Key Enum | -| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------- | +| Year | Rank | Author | Paper | CPU Support | Key Enum | +| ---- | ---- | -------------------------- | ----- | ----------- | --------------------------------------------------------------------------------------------------------------------- | | 2023 | 1st | _Andriy Myronenko, et al._ | TODO | ❌ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_1) | | 2023 | 2nd | _Alyssa R Amod, et al._ | N/A | ❌ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_2) | | 2023 | 3rd | _Ziyan Huang, et al._ | N/A | ✅ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_3) | @@ -92,10 +104,25 @@ For more examples and details please refer to our extensive Notebook tutorials h Meningioma Segmentation
+```python +from brats import MeningiomaSegmenter +from brats.constants import MeningiomaAlgorithms + +segmenter = MeningiomaSegmenter(algorithm=MeningiomaAlgorithms.BraTS23_1, cuda_devices="0") +# these parameters are optional, by default the winning algorithm will be used on cuda: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", +) +``` + **Class:** `brats.MeningiomaSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.MeningiomaSegmenter)) -| Year | Rank | Author | Paper | CPU Support | Key Enum | -| ---- | ---- | -------------------------- | ----- | ----------- | ----------------------------------------------------------------------------------------------------------------------- | +| Year | Rank | Author | Paper | CPU Support | Key Enum | +| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------- | | 2023 | 1st | _Andriy Myronenko, et al._ | N/A | ❌ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_1) | | 2023 | 2nd | _Ziyan Huang, et al._ | N/A | ✅ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_2) | | 2023 | 3rd | _Zhifan Jiang et al._ | N/A | ❌ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_3) | @@ -106,10 +133,25 @@ For more examples and details please refer to our extensive Notebook tutorials h Brain Metastases Segmentation
+```python +from brats import MetastasesSegmenter +from brats.constants import MetastasesAlgorithms + +segmenter = MetastasesSegmenter(algorithm=MetastasesAlgorithms.BraTS23_1, cuda_devices="0") +# these parameters are optional, by default the winning algorithm will be used on cuda: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", +) +``` + **Class:** `brats.MetastasesSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.MetastasesSegmenter)) -| Year | Rank | Author | Paper | CPU Support | Key Enum | -| ---- | ---- | -------------------------- | ----- | ----------- | ----------------------------------------------------------------------------------------------------------------------- | +| Year | Rank | Author | Paper | CPU Support | Key Enum | +| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------- | | 2023 | 1st | _Andriy Myronenko, et al._ | N/A | ❌ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_1) | | 2023 | 2nd | _Siwei Yang, et al._ | N/A | ❌ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_2) | | 2023 | 3rd | _Ziyan Huang, et al._ | N/A | ✅ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_3) | @@ -120,32 +162,66 @@ For more examples and details please refer to our extensive Notebook tutorials h Pediatric Segmentation
+```python +from brats import PediatricSegmenter +from brats.constants import PediatricAlgorithms + +segmenter = PediatricSegmenter(algorithm=PediatricAlgorithms.BraTS23_1, cuda_devices="0") +# these parameters are optional, by default the winning algorithm will be used on cuda: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", +) +``` + **Class:** `brats.PediatricSegmenter` ([Docs](https://brats.readthedocs.io/en/latest/core/segmentation_algorithms.html#brats.core.segmentation_algorithms.PediatricSegmenter)) -| Year | Rank | Author | Paper | CPU Support | Key Enum | -| ---- | ---- | -------------------------- | ----- | ----------- | ---------------------------------------------------------------------------------------------------------------------- | +| Year | Rank | Author | Paper | CPU Support | Key Enum | +| ---- | ---- | -------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------ | | 2023 | 1st | _Zhifan Jiang et al._ | N/A | ❌ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_1) | | 2023 | 2nd | _Andriy Myronenko, et al._ | N/A | ❌ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_2) | | 2023 | 3rd | _Yubo Zhou_ | N/A | ❌ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_3) |
---- +### Inpainting
Inpainting
+```python +from brats import Inpainter +from brats.constants import InpaintingAlgorithms + +inpainter = Inpainter(algorithm=InpaintingAlgorithms.BraTS24_1) +inpainter.infer_single( + t1n="path/to/voided_t1n.nii.gz", + mask="path/to/mask.nii.gz", + output_file="inpainting.nii.gz", +) +``` + **Class:** `brats.Inpainter` ([Docs](https://brats.readthedocs.io/en/latest/core/inpainting_algorithms.html#brats.core.inpainting_algorithms.Inpainter)) -| Year | Rank | Author | Paper | CPU Support | Key Enum | -| ---- | ---- | ----------------------- | ----- | ----------- | ----------------------------------------------------------------------------------------------------------------------- | -| 2023 | 1st | _Juexin Zhang, et al._ | N/A | ✅ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_1) | -| 2023 | 2nd | _Alicia Durrer, et al._ | N/A | ❌ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_2) | -| 2023 | 3rd | _Jiayu Huo, et al._ | N/A | ✅ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_3) | +| Year | Rank | Author | Paper | CPU Support | Key Enum | +| ---- | ---- | ---------------------------------- | ----- | ----------- | ------------------------------------------------------------------------------------------------------------------------- | +| 2024 | 1st | _Ke Chen, Juexin Zhang, Ying Weng_ | N/A | ✅ | [BraTS24_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_1) | +| 2024 | 2nd | _André Ferreira, et al._ | N/A | ❌ | [BraTS24_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_2) | +| 2024 | 3rd | _Team SMINT_ | N/A | ❌ | [BraTS24_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_3) | +| 2023 | 1st | _Juexin Zhang, et al._ | N/A | ✅ | [BraTS23_1](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_1) | +| 2023 | 2nd | _Alicia Durrer, et al._ | N/A | ❌ | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_2) | +| 2023 | 3rd | _Jiayu Huo, et al._ | N/A | ✅ | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_3) |
+>[!TIP] +>For a full notebook examples with more details please check here: +> [![nbviewer](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.org/github/BrainLesion/tutorials/blob/main/BraTS/tutorial.ipynb) + ## Citation If you use BraTS in your research, please cite it to support the development!