This repository contains the implementation of the MICCAI 2021 paper Point-Unet: A Context-Aware Point-Based Neural Network for Volumetric Segmentation. Point-Unet is a point-based volumetric segmentation framework with three main modules: the saliency attention, the context-aware sampling, and the point-based segmentation module. The saliency attention module takes a volume as input and predicts an attentional probability map that guides the context-aware point sampling in the subsequent module to transform the volume into a point cloud. The point-based segmentation module then processes the point cloud and outputs the segmentation, which is finally fused back to the volume to obtain the final segmentation results.
Details of the Point-Unet model architecture and experimental results can be found in our following paper.
@inproceedings{ho2021point,
title={Point-Unet: A Context-Aware Point-Based Neural Network for Volumetric Segmentation},
author={Ho, Ngoc-Vuong and Nguyen, Tan and Diep, Gia-Han and Le, Ngan and Hua, Binh-Son},
booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
pages={644--655},
year={2021},
organization={Springer}
}
Please CITE our paper when Point-Unet is used to help produce published results or incorporated into other software
The code is based on Tensorflow. It has been tested with Python 3.6.9, CUDA 9.0 on Ubuntu 18.04 (NVIDIA V100).
Install required python packages
$ conda env create -f environment.yml
$ sh PointSegment/compile_op.shDownload and organize BraTS18, BraTS19, BraTS20 and Pancreas datasets from their official website. The dataset will be stored at the structure below with nii.gz format
dataset/BraTS2018/
training/
validation/
dataset/BraTS2019/
training/
validation/
dataset/BraTS2020/
training/
validation/
dataset/Pancreas/
ct/
seg/
Available arguments to setup our source code:
optional arguments:
--logdir LOGDIR path to the log directory
--gpu GPU ID
--fold fold ID
--n_epoch number of epoch during training process
--n_point number of point cloud during sample data
--threshold 0.9 threshold to sample data
--mode model of process [train,test]
--inPros_path path to the attention maps
--outBinary_path path to the output binary segmentation
--data_PC_path path to the Point Cloud data
--data_3D_path path to the 3D Volumes data
--checkpoint_path path to the checkpoint of model
--results_path path to the results of Point Cloud segmentation
--outSegment_path path to the final results on 3D Volumes
-
Saliency Attention Map
Train attention maps:
$ python3 SaliencyAttention/train.py \ --logdir SaliencyAttention/model_logs/Pancreas/ \ --gpu 0Predict attention maps:
$ python3 SaliencyAttention/train.py \ --checkpoint_path SaliencyAttention/model_logs/Pancreas/model-50000 \ --gpu 0 \ --predict -
Context-Aware Sampling
Generate Binary Map:
$ python3 utils/genBinaryMap.py \ --inPros_path dataset/Pancreas/attention_maps/ \ --outBinary_path dataset/Pancreas/binary_maps/ \ --threshold 0.9Generate Point Cloud data (Output results are saved with the
*.ply,*pkl,*.npyformat):$ python3 PointSegment/utils/dataPreparePancreas.py \ --n_point 180000 \ --data_3D_path dataset/Pancreas/ \ --outPC_path dataset/Pancreas/PC_data -
PointSegment
Training model:
$ python PointSegment/runPancreas.py \ --gpu 0 \ --mode train \ --fold 3 \ --n_epoch 100 \ --data_PC_path dataset/Pancreas/PC_data \ --logdir PointSegment/model_logs/Pancreas/fold3Evaluation model:
$ python3 PointSegment/runPancreas.py \ --gpu 0 \ --mode test \ --fold 3 \ --data_PC_path dataset/Pancreas/PC_data \ --data_3D_path dataset/Pancreas/ct \ --checkpoint_path PointSegment/model_logs/Pancreas/fold3/snap-497 \ --results_path dataset/Pancreas/Results
Generate Segmentation Results (Output results are saved with the
*.nii.gzformat):$ python3 utils/genSegmentationPancreas.py \ --inPros_path dataset/Pancreas/predict_npy/ \ --outSegment_path dataset/Pancreas/predict_nii \
-
Saliency Attention Map
Train Attention maps:
$ python3 SaliencyAttention/train.py \ --logdir SaliencyAttention/model_logs/BraTS/ \ --gpu 0Predict Attention maps:
$ python3 SaliencyAttention/train.py \ --checkpoint_path SaliencyAttention/model_logs/BraTS/model-50000 \ --gpu 0 --predict -
Context-Aware Sampling
Generate Binary Map:
$ python3 utils/genBinaryMap.py \ --inPros_path dataset/BraTS2020/attention_maps/ \ --outBinary_path dataset/BraTS2020/binary_maps/ \ --threshold 0.9Generate Point Cloud data (Output results are saved with the
*.ply,*pkl,*.npyformat):$ python3 PointSegment/utils/dataPrepareBraTS.py \ --n_point 365000 \ --data_3D_path dataset/BraTS20/ \ --outPC_path dataset/BraTS20/PC_data -
PointSegment
Training model :
$ python3 PointSegment/runBraTS.py \ --gpu 0 \ --mode train \ --n_epoch 100 \ --logdir PointSegment/model_logs/BraTS20 \ --data_PC_path dataset/BraTS2020Evaluation model :
$ python3 PointSegment/runBraTS.py \ --gpu 0 \ --mode test \ --data_PC_path dataset/BraTS2020 \ --checkpoint_path PointSegment/model_logs/BraTS20/snapshots/snap-8261 \ --results_path dataset/BraTS2020/predict_npyGenerate Segmentation Results (Output results are saved with the
*.nii.gzformat):$ python3 utils/genSegmentationBraTS.py \ --inPros_path dataset/BraTS2020/predict_npy/ \ --outSegment_path dataset/BraTS2020/predict_nii \
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Offline validation set
Dataset Dice ET Dice ET Dice ET Average Dice Average HD95 BraTS18 80.76 90.55 87.09 86.13 6.01 BraTS19 85.56 91.18 90.10 88.98 4.92 BraTS20 76.43 89.67 82.97 83.02 8.26 -
Online validation set
Dataset Dice ET Dice ET Dice ET Average Dice Average HD95 BraTS18 80.97 90.50 84.11 85.19 6.30 BraTS19 79.01 87.63 79.70 82.11 10.39 BraTS20 78.98 89.71 82.75 83.81 11.73
This repository is borrow a lot of codes from 3DUnet-Tensorflow-Brats18 and RandLA-Net.
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