Histopathology Image Classification using Deep Manifold Contrastive Learning (MICCAI 2023)

[Paper]

Framework

Tensorflow 2

Dataset

The hepatocellular carcinomas (HCCs) dataset can be downloaded from Pathology AI Platform.

Preprocessing

1. Download the raw WSI data.
2. Prepare the patches.
3. Store all the patches directory in a .csv file (refer patch_list.csv).

Deep Manifold Embedding Learning

Manifold encoder training.

python manifold.py --tr_patch_list [CSV path] --val_patch_list [CSV path] --label_file [CSV path] --save_dir [folder path] --num_class 2 --num_NN 5 --num_cluster 10 --save_model_dir [folder path]

Bag formation

1. Generate bag list in bag_list.csv.

python bag_list_generation.py --tr_patch_list [CSV path] --val_patch_list [CSV path] --te_patch_list [CSV path] --save_dir [folder path] --num_bag 50 --num_patchPerbag 100 

2. Feature extration based on bag_list.csv. Example of split_file.csv is in split_file.csv.

python feature_extraction.py --bag_list_dir  [CSV path]  --split_file [CSV path] --ckpt_dir [checkpoint path] --save_dir [folder path] --src_dir [folder_path]

MIL training

Train simple MIL for classification.

 python mil.py --feat_dir  [folder path]  --label_file [CSV path] --num_class 2 --save_model_dir [CSV path]

Citation

Please cite us if you use our work.