YoloV8 model for the segmentation of the lungs in mice CT scans.
Project description
🫁 Lungs segmentation in mice CT scans
We provide a YoloV8 model for the segmentation of the lungs region in mice CT scans. The model was trained on 2D slices and can be applied slice by slice to produce 3D segmentations.
[Installation
] [Model weights
] [Usage
]
This project is part of a collaboration between the EPFL Center for Imaging and the De Palma Lab.
Installation
We recommend performing the installation in a clean Python environment. Install our package from PyPi:
pip install mouselungseg
or from the repository:
pip install git+https://gitlab.com/center-for-imaging/lungs-segmentation.git
or clone the repository and install with:
git clone git+https://gitlab.com/center-for-imaging/lungs-segmentation.git
cd mouselungseg
pip install -e .
Model weights
The model weights (~6 Mb) are automatically downloaded from this repository on Zenodo the first time you run inference. The model files are saved in the user home folder in the .mousetumornet
directory.
Usage
In Napari
To use our model in Napari, start the viewer with
napari -w mouselungseg
Open an image using File > Open files
or drag-and-drop an image into the viewer window.
Sample data: To test the model, you can run it on our provided sample image. In Napari, open the image from File > Open Sample > Mouse lung CT scan
.
Next, in the menu bar select Plugins > Lungs segmentation (mouselungseg)
to start our plugin.
As a library
You can run a model in just a few lines of code to produce a segmentation mask from an image (represented as a numpy array).
from mouselungseg import LungsPredictor
lungs_predict = LungsPredictor()
segmentation = lungs_predict.predict(your_image)
As a CLI
Run inference on an image from the command-line. For example:
uls_predict_image -i /path/to/folder/image_001.tif
The command will save the segmentation next to the image:
folder/
├── image_001.tif
├── image_001_mask.tif
To run inference in batch on all images in a folder, use:
uls_predict_folder -i /path/to/folder/
This will produce:
folder/
├── image_001.tif
├── image_001_mask.tif
├── image_002.tif
├── image_002_mask.tif
Issues
If you encounter any problems, please file an issue along with a detailed description.
License
This model is licensed under the BSD-3 license.
Related projects
- Mouse Tumor Net | 3D U-Net model trained to segment tumor nodules in mice CT scans.
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