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