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Add code example per algorithm
Add nb viewer badge
Add Inpainting 2024 algos to table
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@MarcelRosier
MarcelRosier committed Nov 29, 2024
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Expand Up @@ -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
<details open>

<summary> <strong> Adult Glioma Segmentation </strong> </summary>
<br>


```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
Expand All @@ -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

<details open>

<summary> <strong> Adult Glioma Segmentation </strong> </summary>
<br>

**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) | &#x274C; | [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 | &#x274C; | [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 | &#x274C; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AdultGliomaAlgorithms.BraTS23_3) |
Expand All @@ -78,10 +75,25 @@ For more examples and details please refer to our extensive Notebook tutorials h
<summary> <strong> BraTS-Africa Segmentation </strong> </summary>
<br>

```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 | &#x274C; | [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 | &#x274C; | [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 | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.AfricaAlgorithms.BraTS23_3) |
Expand All @@ -92,10 +104,25 @@ For more examples and details please refer to our extensive Notebook tutorials h
<summary> <strong> Meningioma Segmentation </strong> </summary>
<br>

```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 | &#x274C; | [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 | &#x2705; | [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 | &#x274C; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MeningiomaAlgorithms.BraTS23_3) |
Expand All @@ -106,10 +133,25 @@ For more examples and details please refer to our extensive Notebook tutorials h
<summary> <strong> Brain Metastases Segmentation </strong> </summary>
<br>

```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 | &#x274C; | [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 | &#x274C; | [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 | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.MetastasesAlgorithms.BraTS23_3) |
Expand All @@ -120,32 +162,66 @@ For more examples and details please refer to our extensive Notebook tutorials h
<summary> <strong> Pediatric Segmentation </strong> </summary>
<br>

```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 | &#x274C; | [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 | &#x274C; | [BraTS23_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_2) |
| 2023 | 3rd | _Yubo Zhou_ | N/A | &#x274C; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.PediatricAlgorithms.BraTS23_3) |

</details>

---
### Inpainting

<details>
<summary> <strong> Inpainting </strong> </summary>
<br>

```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 | &#x2705; | [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 | &#x274C; | [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 | &#x2705; | [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 | &#x2705; | [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 | &#x274C; | [BraTS24_2](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS24_2) |
| 2024 | 3rd | _Team SMINT_ | N/A | &#x274C; | [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 | &#x2705; | [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 | &#x274C; | [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 | &#x2705; | [BraTS23_3](https://brats.readthedocs.io/en/latest/utils/utils.html#brats.utils.constants.InpaintingAlgorithms.BraTS23_3) |

</details>

>[!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!
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