QLFM

matlab code for "Computational optical sectioning with an incoherent multiscale scattering model for light-field microscopy" Version: 1.0 Copyright: 2021, YI ZHANG, ZHI LU, JIAMINWU, XING LIN, DONG JIANG, YEYI CAI, JIACHEN XIE, YULING WANG, TIANYI ZHU, XIANGYANG JI, QIONGHAI DAI

Contents

• Overview
• Directory structure
• How to use
• Citation

Overview

This repository provides the implementation of the QLFM reconstruction with different models, including QLFM without scattering using ideal PSFs, QLFM without scattering using calibrated PSFs, QLFM with alternating scattering directions.

Additional example data and experimental PSFs can be downloaded with the following link: https://drive.google.com/drive/folders/1bTH5eibetRsKuxwTPZk9sAXzOvdA2wgf?usp=sharing

Directory structure

QLFM
|---recon_main
|---|---backwardProjectACC_fft2.m
|---|---deconvGPU_QLFMScatter_2D.m
|---|---deconvGPU_QLFMScatter_L2R.m
|---|---deconvGPU_QLFMScatter_R2L.m
|---|---deconvGPU_QLFMwithoutScatter.m
|---|---forwardProjectACC_fft2.m
|---|---imwrite3dTIFF.m
|---|---main.m
|---|---map.mat
|---|---SampleV.m
|---|---Recon_QLFMwithoutScatter_cali
|---|---|---c1_frame0.tif
|---|---Recon_QLFMwithoutScatter_ideal
|---|---|---c1_frame0.tif
|---|---Recon_QLFMwithScatter_2directions
|---|---|---c1_frame0.tif
|---|---Recon_QLFMwithScatter_Left2Right
|---|---|---c1_frame0.tif
|---|---Recon_QLFMwithScatter_Right2Left
|---|---|---c1_frame0.tif
|---psf
|---|---index.mat
|---|---psf_cali2.mat
|---|---psf_ideal2.mat
|---|---readme.md
|---dataset
|---|---c1-1.tif
|---|---readme.md
|---README.md

How to use

Environment

• MATLAB 2020b (64bit)
• Windows 10 64bit
• Intel i9-9820X CPU
• NVIDIA TITAN RTX GPU
• 128G RAM

Steps

1. Unpack the package
2. According to the instructions in the readme file in the psf folder, download the psf data.
3. According to the instructions in the readme file in the dataset folder, download the sub-aperture data.
4. Run the main.m file in the recon_main folder. In the main.m, there are 5 reconstruction models to choose from:

• QLFM_ideal: QLFM without scattering, using ideal psf
• QLFM_cali: QLFM without scattering, using calibrated psf
• QLFM_sca_LTR: QLFM with forward scattering
• QLFM_sca_RTL: QLFM with backward scattering
• QLFM_sca_2D: QLFM with forward and backward scattering

Reconstructed results can be downloaded from the folowing link: https://drive.google.com/drive/folders/1s26POd00MrbyqtA2pXGxOoHswrqZKXNL?usp=sharing

Citation

If you use the code, please cite the companion paper where the original method appeared: Zhang, Y. et al. Computational optical sectioning by phase-space imaging with an incoherent multiscale scattering model. Nature communications(2021) doi:10.1038/s41467-021-26730-w.