matthewachan/fpm_inr

Fourier Ptychographic Microscopy Reconstruction using Implicit Neural Representation

FPM_INR

FPM-INR Fourier Ptychographic Microscopy Image Stack Reconstruction using Implicit Neural Representation

The full version of the code has been released.

Paper link: https://doi.org/10.1364/OPTICA.505283

Project page: https://hwzhou2020.github.io/FPM-INR-Web/

arXiv: https://arxiv.org/abs/2310.18529

Data source: https://doi.org/10.22002/7aer7-qhf77

Top-level folder structure:

.
├── data                    # File path for raw / preprocessed FPM data
├── FPM_Matlab              # Matlab code for FPM with first-order optimization (Parallel computing toolbox needed)
├── func                    # All-in-focus computation using LightField method or normal variance method
├── scripts                 # Scripts to run FPM-INR
├── trained_models          # reults save directory
├── vis                     # Result visualization
├── environment.txt         # Anaconda environment
├── FPM_INR.py              # Main Python script
├── FPM_INR_thyroid.py      # Main Python script for thyroid samples
├── network.py              # INR neural network
├── unils.py                # Utility functions
└── README.md

The thyroid sample was acquired from a different system setup compared to other samples. For convenience, we put it in a different python script. This is a demostration that our method is not limited to a specific FPM system setting and can be generaized to different FPM systems.

Dependency

apt update && apt install -y wget git vim pip

pip install -U matplotlib

pip install -U scikit-image

pip install mat73

To use torch.compile '--is_system Linux', pytorch version >= 2.0.0

If only use torch.jit '--is_system Windows', pytorch version can be 1.xx.x

Example of pytorch:

conda install pytorch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 pytorch-cuda=11.8 -c pytorch -c nvidia

Additional anaconda environment.yml file is provided

Download data

Data source: https://doi.org/10.22002/7aer7-qhf77

Example:

wget https://data.caltech.edu/records/7aer7-qhf77/files/Siemens_r.mat

Erratum for data file name

Please rename BloodSmearTilt_g.mat to BloodSmearTilt_r.mat

Please rename BloodSmearTilt_g_GT.mat to BloodSmearTilt_r_GT.mat

Docker file

Docker container is available at

docker pull hwzhou/inr-repo:fpm-inr

BiBTeX

@article{Zhou2023fpminr,
  author = {Haowen Zhou and Brandon Y. Feng and Haiyun Guo and Siyu (Steven) Lin and Mingshu Liang and Christopher A. Metzler and Changhuei Yang},
  journal = {Optica},
  keywords = {Biomedical imaging; Computer simulation; Deep learning; Neural networks; Phase retrieval; Systems design},
  number = {12},
  pages = {1679--1687},
  publisher = {Optica Publishing Group},
  title = {Fourier ptychographic microscopy image stack reconstruction using implicit neural representations},
  volume = {10},
  month = {Dec},
  year = {2023},
  url = {https://opg.optica.org/optica/abstract.cfm?URI=optica-10-12-1679},
  doi = {10.1364/OPTICA.505283}
}