The Pytorch implementation of our MLMI19 oral paper WSI-Net: Branch-based and Hierarchy-aware Network for Segmentation and Classification of Breast Histopathological Whole-slide Images.

Python 2.7, Pytorch 1.0.0, opencv, libtiff, tensorboardX, etc.

Our benchmark dataset is provided by Xiangya Hospital, Central South University, which is still a private dateset now. The detailed description of our dataset can be found in our paper. You may also utilize the other similar public datasets, such as BACH, Camelyon16 and Camelyon17.

Our models mainly include: the original DeepLab, DeepLab-HA (DeepLab plus our hierarchy-aware loss), BranchNet (DeepLab plus our classification branch), and WSI-Net (DeepLab-HA plus our classification branch).

We borrow the code of DeepLab from this link.

For training DeepLab, we first utilize XY3_Cut_1280_train_patch.py to preprocess each whole-slide image (WSI) to remove non-tissue areas and divide it into multiple training patches. This code will also generate the train.txt for training.

Subsequently, we train our baseline DeepLab model. The implementation details about this model can be found in Pytorch-Deeplab/deeplab/model.py. Please run Pytorch-Deeplab/train.py to perform the training process.

DeepLab-HA is actually training DeepLab with traditional pixel-wise loss plus our proposed hierarchy-aware loss. The training process is very similar to training DeepLab, except running Pytorch-Deeplab/train_plus_label_constraint.py instead of train.py.

BranchNet is DeepLab plus classification Branch. The preprocessing and patch dividing is similar to part A and Part B.

When training, we first train DeepLab for 1 epoch from pretrained model. Then we fix it and only train our classification branch for 25 epochs. This process can be implemented by running Pytorch-Deeplab/train_initial_check.py. Note that when training branch part, we need the patch with the size of 4096*4096. So please change the parameter setting in XY3_Cut_1280_train_patch.py to generate these patches. Subsequently, we later jointly train DeepLab and classification branch for 9 epochs by running Pytorch-Deeplab/train_jointly_wo_patch_loss.py.

WSI-Net is DeepLab-HA plus classification Branch. The training process is very similar to that of BranchNet, except training DeepLab-HA instead of DeepLab in the beginning, and finally run Pytorch-Deeplab/train_jointly.py to jointly train DeepLab-HA and branch.

The testing processes include dividing WSI testing patches, performing inference on each testing patches, merging testing patches results into the single WSI segmentation results, and finally extracting feature from WSI and performing classification.

Firstly, please run XY3_divide_test_patch.py to divide WSI into testing patches.

Secondly, please run Pytorch-Deeplab/evaluate.py to perform inference using DeepLab or DeepLab-HA. please run Pytorch-Deeplab/test_initial_check.py to perform inference using BranchNet or WSI-Net. You can use SaveHeatmapAndMask.py to visualize the patch segmentation results.

Thirdly, please run merge_npz_final.py to merge testing patches results into the single WSI segmentation results. You can use SaveWholeHeatmapAndMask.py to visualize the WSI segmentation results.

Finally, please run ExtraFeatureFromMap.py to extract WSI feature and perform WSI segmentation. You can use Metrics.py or Bootstrap_metrics.py (used in our paper) for performance evaluation.

More details can also be found in our supplementary file.

If you find our approaches useful in your research, please consider citing:

@inproceedings{ni2019wsi,
  title={WSI-Net: Branch-Based and Hierarchy-Aware Network for Segmentation and Classification of Breast Histopathological Whole-Slide Images},
  author={Ni, Haomiao and Liu, Hong and Wang, Kuansong and Wang, Xiangdong and Zhou, Xunjian and Qian, Yueliang},
  booktitle={International Workshop on Machine Learning in Medical Imaging},
  pages={36--44},
  year={2019},
  organization={Springer}
}

For any problems with the code, please feel free to contact me: homerhm.ni@gmail.com

We acknowledge the code about DeepLab from speedinghzl.