RAPHIA

Official implementation of:

Wei Shao et al. "RAPHIA: A deep learning pipeline for the registration of MRI and whole-mount histopathology images of the prostate." [Computers in Biology and Medicine)]

Requirements

• pip install -r requirements.txt

Dataset

• For demonstration purposes, we use the public TCIA dataset: https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=23691514

Usage

Step 1. Download the pre-trained model:

• Obtain the pre-trained models using this link

Step 2. Set up the image registration json files and histology json files

Step 3. Run the following Jupyter notebook for automated image registration:

• RAPHIA.ipynb

BibTeX

If you use this code, please cite the following paper:

@article{shao2024raphia,
  title={RAPHIA: A deep learning pipeline for the registration of MRI and whole-mount histopathology images of the prostate},
  author={Shao, Wei and Vesal, Sulaiman and Soerensen, Simon JC and Bhattacharya, Indrani and Golestani, Negar and Yamashita, Rikiya and Kunder, Christian A and Fan, Richard E and Ghanouni, Pejman and Brooks, James D and others},
  journal={Computers in Biology and Medicine},
  pages={108318},
  year={2024},
  publisher={Elsevier}
}