This repository is for Simplified SACD (w/o Sparse deconvolution) and will be in continued development. It is a part of publication. For details, please refer to: [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.
## SACD demo
These two demos can be found at the [release v1.1.3](https://github.com/WeisongZhao/SACDj/releases/tag/v1.1.3). ## Instruction - Tips: Regarding the SACD SR frame visualization, it can be scaled with a gamma correction according to the bSOFI setting. ```python In FIJI/ImageJ: Process->Math->gamma(0.5) Process->Filters->Gaussian Blur(1) Process->Enhance Contrast(0%; normalize) Macro: run("Gamma...", "value=0.50"); run("Gaussian Blur...", "sigma=1"); run("Enhance Contrast...", "saturated=0 normalize"); ``` - Tips: If data contains strong background, a pre background subtraction will help. ```python In FIJI/ImageJ: Process->Subtract background ``` ## Declaration This repository contains the java source code (Maven) for SACD imagej plugin. This plugin is for the Simplified SACD (w/o Sparse deconvolution), and is also accompanied with conventional SOFI reconstruction ; RL deconvolution; and PSF calculation features. The development of this imagej plugin is work in progress, so expect rough edges. If you want to reproduce the results of SACD publication, the [SACDm](https://github.com/WeisongZhao/SACDm) (Matlab version) is recommended. Due to the distance between the Fourier interpolation, deconvolution of SACDj, and SACDm, there may exist a gap between the results of SACDm and SACDj. For me, the implementations of SACDm are more flexible and accurate. ## Version - v1.1.3 Fixed for memory recycle & 20 times execution acceleration - v1.1.0 Useful tools separated: RL deconvolution, PSF calculation, SOFI reconstruction & Fourier interpolation - v1.0.0 Simplified SACD - v0.6.0 Accelerated RL-TV deconvolution - v0.5.0 Accelerated RL deconvolution - v0.4.0 Born-Wolf PSF - v0.3.0 SACD core - v0.2.0 Fourier interpolation - v0.1.0 Cumulant reconstruction core ## Related links: - MATLAB version of SACD: [SACDm](https://github.com/WeisongZhao/SACDm) - **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)