ACsN

ACsN (pronounced as action) stands for Automatic Correction of sCMOS-related Noise. It combines an accurate estimation of noise variation with sparse filtering to eliminate the most relevant noise sources in the images of a sCMOS sensor. This results in a drastic reduction of pixel-dependent noise in sCMOS images and an enhanced stability of denoising performance at a competitive computational speed.

Citation

Please, cite our paper on Nature Communications.

Mandracchia, B., Hua, X., Guo, C. et al. Fast and accurate sCMOS noise correction for fluorescence microscopy. Nat Commun 11, 94 (2020) doi:10.1038/s41467-019-13841-8

System Requirements

Hardware Requirements

ACsN requires a standard computer with enough RAM to support MATLAB 2014b. For minimal performance, this will be a computer with about 2 GB of RAM. For optimal performance, we recomend the following specs:

RAM: 16+ GB; CPU: 6+ cores, 3.2+ GHz/core.

Software Requirements

MATLAB 2014b+

MATLAB 2018a+ (Graphic interface)

MATLAB "Curve Fitting" Toolbox

Windows OS 7+

Install

Graphic Interface

To run ACsN graphic interface:

• Double-click the ACsN.mlappinstall file in the ACsN_matlab_app folder.
• In MATLAB, go to App>My App and double-click on ACsN.
• To test the program you can use the images provided in the Test Images folder. See the file Settings.txt for the aquisition parameters.

MATLAB Command Line

To run ACsN from MATLAB command line:

• Add the folder ACsN_code to your MATLAB path (including subfolders).
• In the command line type help ACSN or run the Sample code script in the Test Images folder to see the code usage.

ImageJ/Fiji

To run ACsN from ImageJ/Fiji follow these steps:

• Add the ImageJ-MATLAB update site to ImageJ. To see how, look at here.
• Go to Edit > Options > MATLAB and enter the file path for MATLAB licence.
• Add the ACsN_code folder and subfolders to the MATLAB path.
• Copy the file 'ACsN_.m' to the folder '\plugins\Scripts\Process'.
• Select an open image in ImageJ and then press Process > ACsN from the menu toolbar.
• To test the program you can use the images provided in the Test Images folder. See the file Settings.txt for the aquisition parameters.

The installation on a recommended computer should take less than 3 seconds.