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WSI-VQA: Interpreting Whole Slide Images by Generative Visual Question Answering [ECCV 2024]

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Arxiv

Summary We propose a framework to achieve WSI-VQA. It helps pathologists to obtain the result of carcinoma grading, immunohistochemical biomarker prediction, and survival outcome prediction following the visual question-answering pattern. We also propose a scalable pipeline to automatically curate VQA pairs for whole slide images. The WSI-VQA dataset <a href="https://drive.google.com/file/d/1l8XUgDKgzDCZzneLG7PZFbUmL9NP7GhF/view?usp=drive_link" target="blank"><b>Train Set</b></a> |<a href="https://drive.google.com/file/d/1Z6ueneNWgOSfP940HoBCPYAwn2riYkss/view?usp=drive_link" target="blank"><b>Val Set</b></a> |<a href="https://drive.google.com/file/d/1eSQaZ-hKRUDCerGKkPW8VtfOQPgFOMD7/view?usp=drive_link" target="blank"><b>Test Set</b></a> is now available here. The <a href="https://drive.google.com/file/d/16Pp4qVI32se2h8nOpcY6Wbf_fTNviExz/view?usp=sharing" target="blank"><b>checkpoint</b></a> (resnet feature as the input) is also provided now.

Pre-requisites:

We will share our collected dataset but WSIs still need to be preprocessed due to their large resolution. For a quick start, we provide several WSI features after processing in the repository. You can now download our code and directly run the code.

Downloading TCGA Slides

To download diagnostic WSIs (formatted as .svs files), please refer to the NIH Genomic Data Commons Data Portal. WSIs for each cancer type can be downloaded using the GDC Data Transfer Tool.

Processing Whole Slide Images

To process WSIs, first, the tissue regions in each biopsy slide are segmented using Otsu's Segmentation on a downsampled WSI using OpenSlide. The 256 x 256 patches without spatial overlapping are extracted from the segmented tissue regions at the desired magnification. Consequently, a pretrained backbone is used to encode raw image patches into feature vectors, which we then save as .pt files for each WSI. We achieve the pre-processing of WSIs by using <a href="https://github.com/mahmoodlab/CLAM" target="blank"><b>CLAM</b></a>

Data Arrangement

Put WSI features under ./dataset/WSI_features

Put our provided files (WsiVQA_*.json) under ./dataset/WSI_captions

Environment

* Linux (Tested on Ubuntu 18.04) 
* NVIDIA GPU (Tested on Nvidia GeForce A100) with CUDA 12.0
* Python==3.8
* torch==1.10.0+cu111
* torchvision==0.11.0+cu111
* pycocoevalcap==1.2
* pycocotools==2.0.7
* transformers==4.33.3

Running Experiments

Experiments can be run using the following generic command-line:

Training model

python main.py --mode 'Train' --n_gpu <GPUs to be used, e.g '0,1,2,3' for 4 cards training> 

Testing model

python main.py --mode 'Test' --image_dir <SLIDE FEATURE PATH> --ann_path <CAPTION PATH> --split_path <PATH to the directory containing the train/val/test splits> --checkpoint_dir <PATH TO CKPT>

Downstream Evaluation

Refer to ./downstream/show.ipynb

Examples

Several examples of the WSIs and their corresponding VQA pairs. The pairs in the grey rectangle are from the close-ended subset which has multiple choices while the ones in the blue rectangle are from the open-ended subset. The choice which is underlined is the right answer. These questions are all challenging because they require sufficient medical knowledge and understanding of complex characteristics in the gi- gapixel WSIs.

Citation

If you find our work useful in your research or if you use parts of this code please consider citing our paper:

@inproceedings{chen2025wsi,
  title={Wsi-vqa: Interpreting whole slide images by generative visual question answering},
  author={Chen, Pingyi and Zhu, Chenglu and Zheng, Sunyi and Li, Honglin and Yang, Lin},
  booktitle={European Conference on Computer Vision},
  pages={401--417},
  year={2025},
  organization={Springer}
}