Work in progress
This repository is the code associated with the engineering thesis "Learning-Based Staining Normalization for Improving Registration of Histology Images".
This presents our try to evaluate deep learning approaches in stain normalization as a preprocessing step in image registration.
Keep in mind we are currently streamlining this process
For affine alignment configure and run AffineClicker/main.py. Click through all the images and save the list.
Then run AffineClicker/affine_trans.py to generate a summary table of the dataset with additional affine alignment matrices.
For trainig the deep learning model make your configuration in HistNet/config.py and run HistNet/train.py
For HPC (SLURM) we provide run_hpc.slurm file that lets you configure and easily run training with live tensorboard tunneling through ssh.
Dataset provided by the ANHIR Grand Challenge organizers and is available here
- PyTorch
- NumPy
- Matplotlib
- Torchio
- Kornia
- Pandas
- OpenCV