Add 3D semantic segmentation code example#2092
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innat-asj wants to merge 1 commit intokeras-team:masterfrom
Closed
Add 3D semantic segmentation code example#2092innat-asj wants to merge 1 commit intokeras-team:masterfrom
innat-asj wants to merge 1 commit intokeras-team:masterfrom
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mattdangerw
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May 1, 2025
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mattdangerw
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Looks good thanks! Just some comments on avoiding google drive.
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| These region-wise groupings allow for evaluation across different tumor structures relevant for clinical assessment and treatment planning. A sample view is shown below, figure taken from [BraTS-benchmark](https://arxiv.org/pdf/2107.02314v1) paper. | ||
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we should move any assets out of a personal drive. there should be examples of guide assets elsewhere on keras.io
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| from medicai.utils.inference import SlidingWindowInference | ||
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| In this [Kaggle notebook](https://www.kaggle.com/code/ipythonx/3d-brats-segmentation-in-keras-multi-gpu/) (version 2), we trained the model on the entire dataset for approximately 25 epochs. The resulting weights will be used for further evaluation. Note that the validation set used in both the Colab and Kaggle notebooks is the same: `training_shard_36.tfrec`, which contains `8` samples. We will be evaluating the model per-class and on average. | ||
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| model_weight = gdown.download(id="1b-DpZkMsAX6I-niuLu7h8_y3XiaSHFyN", quiet=False) |
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could you just upload these to kaggle? nice than gdown here (and we are already using kaggle)
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I've built a medical ai toolkit for 3d segmentation using keras 3. https://github.com/innat/medic-ai (
medicai). Using this I've implemented a complete workflow for 3d medical imaging end-to-end training. Themedicaiis greatly inspired bymonai, which mainly works in torch ecosystem.Now, using this toolkit, I've implemented this code example for multi-modal brain tumor segmentation task. Please let me know if it is suitable to add in keras code example.