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https://github.com/weisongzhao/sacdm
Official MATLAB implementation of the "SACD" -v0.2.0
https://github.com/weisongzhao/sacdm
Last synced: 25 days ago
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Official MATLAB implementation of the "SACD" -v0.2.0
- Host: GitHub
- URL: https://github.com/weisongzhao/sacdm
- Owner: WeisongZhao
- License: odbl-1.0
- Created: 2021-08-11T16:30:50.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-02-08T08:42:07.000Z (9 months ago)
- Last Synced: 2024-02-08T09:38:58.914Z (9 months ago)
- Language: MATLAB
- Homepage:
- Size: 5.87 MB
- Stars: 14
- Watchers: 2
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
[](https://github.com/WeisongZhao/SACDm/)
[](https://github.com/WeisongZhao/SACDm/releases/tag/v0.2.0/)
[](https://github.com/WeisongZhao/SACDm/blob/master/LICENSE.txt)
[](https://github.com/WeisongZhao/SACDm/releases/tag/v0.2.0/)
[](https://doi.org/10.1038/s41566-023-01234-9)
[](https://engineeringcommunity.nature.com/posts/super-resolution-made-easier)
[](https://twitter.com/search?q=%23SACDimaging&src=hashtag_click)
[](https://github.com/WeisongZhao/SACDm/)
[](https://github.com/WeisongZhao/SACDm/)
[](https://github.com/WeisongZhao/SACDm/)
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)](https://doi.org/10.1038/s41566-023-01234-9). Please cite SACD in your publications, if it helps your research.
The related FIJI/ImageJ plug-in version can be found at [HERE](https://github.com/WeisongZhao/SACDj/)
You can also find some fancy results and comparisons on my [website](https://weisongzhao.github.io/home/portfolio-4-col.html#SACD).
If you are interested in our work, I wrote a [#behind_the_paper](https://engineeringcommunity.nature.com/posts/super-resolution-made-easier) 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:
```python
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.
```python
addpath(genpath('SACDm'));
help SACDm
```
- Regarding the SACD SR frame visualization, it can be scaled with a gamma correction according to the bSOFI setting.
```python
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](https://github.com/WeisongZhao/SACDj/releases/tag/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](https://github.com/WeisongZhao/SACDj).
## Version
- v0.2.0 Sparse-SACD reconstruction core
- v0.1.0 SACD reconstruction core
## Related links:
- ImageJ plug-in version of SACD: [SACDj](https://github.com/WeisongZhao/SACDj)
- **Some fancy results and comparisons:** [my website](https://weisongzhao.github.io/home/portfolio-4-col.html#SACD)
- **Preprint:** [Weisong Zhao et al. Enhancing detectable fluorescence fluctuation for high-throughput and four-dimensional live-cell super-resolution imaging, bioRxiv (2022).](https://doi.org/10.1101/2022.12.12.520072)
- **Reference:** [Weisong Zhao et al. Enhanced detection of fluorescence fluctuation for high-throughput super-resolution imaging, Nature Photonics (2023)](https://doi.org/10.1038/s41566-023-01234-9)
Plans
- Full FRC-assisted SACD;
- Full 3D-SACD;
- GPU acceleration.
## Open source [SACDm](https://github.com/WeisongZhao/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.