Skip to content

Official MATLAB implementation of the "SACD" -v0.2.0

License

Notifications You must be signed in to change notification settings

WeisongZhao/SACDm

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

38 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Github commit Github All Releases License releases
paper post
Twitter GitHub watchers GitHub stars GitHub forks

SACDm

Fater super-resolution fluctuation imaging: SACD reconstruction with MATLAB.
v0.2.0



This repository is for SACD reconstruction, and it will be in continued development. It is distributed as accompanying software for publication: Weisong Zhao et al. Enhanced detection of fluorescence fluctuation for high-throughput super-resolution imaging, Nature Photonics (2023). Please cite SACD in your publications, if it helps your research.






The related FIJI/ImageJ plug-in version can be found at HERE

You can also find some fancy results and comparisons on my website.

If you are interested in our work, I wrote a #behind_the_paper post for further reading.

SACD reconstruction

Instruction

  • The SACD reconstruction requires resolution-related parameter to execute deconvolution, you can give it with objective-NA; wavelength (nm); and pixel-size (nm), or just provide resolution and pixel-size, or feed it with your own-PSF. Here are 3 examples:
SRimg = SACDm(imgstack, 'pixel', 65, 'NA', 1.3, 'wavelength', 561);
SRimg = SACDm(imgstack, 'pixel', 65, 'resolution', 250);
SRimg = SACDm(imgstack, 'psf', ownpsf);
  • Please try help to get the API.
addpath(genpath('SACDm')); 
help SACDm
  • Regarding the SACD SR frame visualization, it can be scaled with a gamma correction according to the bSOFI setting.
background = 0.02; order = 2;
SRimg2vis = real(SRimg.^0.5);
SRimg2vis(SRimg2vis < order * background * max(SRimg2vis(:))) = 0;
figure(2);imshow(SRimg2vis, [], 'colormap', hot)

Two demos can also be found at the SACDj release v1.1.3.

Declaration

This repository contains the MATLAB source code for SACD .

If you are not a MATLAB user, you can have a try on the imagej version of SACD: SACDj.



Version

  • v0.2.0 Sparse-SACD reconstruction core
  • v0.1.0 SACD reconstruction core

Related links:

Plans
  • Full FRC-assisted SACD;
  • Full 3D-SACD;
  • GPU acceleration.

Open source SACDm

This software and corresponding methods can only be used for non-commercial use, and they are under Open Data Commons Open Database License v1.0.

About

Official MATLAB implementation of the "SACD" -v0.2.0

Resources

License

Stars

Watchers

Forks

Packages

No packages published