This repository contains the code for Journal of Biomedical Optics paper with the same name. This repo also contains additional code and results for denoising 2D simulations + additional test cases for both 2D and 3D.

All required Python packages can be installed via requirements.txt:

pip install -r requirements.txt

Matlab also must be installed for generating datasets required for training and testing. MCXLab and other supporting Matlab mex files are already included in this repository. There is no need to additionally clone the required files, unless you want a newer version of MCX/MCXLab. They are located in the matlab/ folder.

To generate both training and testing dataset, run Matlab function generate_data included in data/generate/generate_data.m. More info on the arguments can be found in the file itself.

To train, run train-lightning.py with the configs in the 2D and 3D folder. Refer to config.py for more info on the config arguments.

Run model-inference.py for model inference with configs in the 2D and 3D folder. Refer to config.py for more info on the config arugments.

• configs/ contains all the yaml configurations needed to run scripts
  • 2D+3D/ contains all configurations for 2D/3D fluence maps
    • analysis/ contains all configurations for analysing inference results from all models
      • cross-section contains all configuration for analysing the middle cross-section of benchmarks B1-B3.
      • global-metrics contains all configurations for analysing the global metrics (MSE, PSNR, SSIM) for all benchmarks in the paper.
    • blind-denoising contains all configurations for training denoising models.
    • inference contains all configurations for performing inference on different datasets using different models.
    • profile (3D only) contains all configurations for profiling the denoising models on different dataset dimensions presented in the paper.
    • visualization contains all configurations for visualizing the results acquired from denoising.
• data/
  • augmentation/ contains logic used for data augmentation during training.

If you use this work in your publication, please cite the following: