https://github.com/esoubies/sim_reconstruction

Single-slice structured illumination microscopy (SIM) reconstruction algorithm based on an inner-loop-free ADMM. This method enables the estimation of the out-of-focus signal that usually affects the reconstructions obtained from 2D acquisitions.
https://github.com/esoubies/sim_reconstruction

Last synced: about 1 month ago
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Single-slice structured illumination microscopy (SIM) reconstruction algorithm based on an inner-loop-free ADMM. This method enables the estimation of the out-of-focus signal that usually affects the reconstructions obtained from 2D acquisitions.

• Host: GitHub
• URL: https://github.com/esoubies/sim_reconstruction
• Owner: esoubies
• License: gpl-3.0
• Created: 2020-10-28T08:55:52.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2020-12-02T14:43:18.000Z (about 4 years ago)
• Last Synced: 2023-10-19T22:59:08.614Z (over 1 year ago)
• Language: MATLAB
• Homepage:
• Size: 60.5 MB
• Stars: 6
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# SIM_Reconstruction

## Description

Structured illumination microscopy (SIM) reconstruction algorithm with computational sectioning.  More details can be found in the following paper:

[1] Computational Super-Sectioning for Single-Slice Structured Illumination Microscopy., 


IEEE Transactions on Computational Imaging, vol. 5 no. 2, pp. 240-250, 2019.  


E. Soubies, and M. Unser.

## Requirements

The code requires the GlobalBioIm library v1.1.2 (or more recent releases) 


https://biomedical-imaging-group.github.io/GlobalBioIm/

## Repository content

The repository is organized as follows.

- The script **SimScript2D.m** contains the main code of the method proposed in [1].

- The script **SimuSIM2D.m** allows to generate 2D-SIM data (used in ScriptSimuExample.m).

- The script **ScriptFig3.m** reproduces the Figure 3 of [1].

- The script **ScriptSimuExample.m** is an example on a small simulated example without out-of-focus signal.

- The script **ScriptRealExample.m** is an example on the real SIM data located within the folder Data/.

- The script **ScriptPatternFromFairSIM.m** provides an example on how to generate images of the patterns given the xml file that can be obtained with  FairSIM 

- Folder **Data** contains raw-SIM data with corresponding (estimated) PSF and patterns generated as explained in ScriptPatternFromFairSIM.m

- Folder **Utils** contains auxilliary functions