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YPZ858 / Super-res-code

For super resolution imaging analysis
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Code zip #1

Open YPZ858 opened 2 years ago

YPZ858 commented 2 years ago

SPA.zip

YPZ858 commented 2 years ago

This code is developed for the reconstruction of single-molecule localisation based super-resolution images.

The drift correction, image reconstruction, and morphology analysis was performed by mean shift algorithm(1), ThunderSTORM(2), and morphology library(3), respectively.

Before processing, make sure you have:

  1. Matlab, with add-on of MIJ, Curve fitting toolbox, MATLAB support for MinGW-w64 C/C++ compiler and statistic and machine learning toolbox.
  2. FIJI or ImageJ with plug-in of morphology library and ThunderSTORM.

Usage: Extract the files from the zip to a desired location. Add the mij.jar from your imageJ/FIJI to the java folder in your Matlab folder. Open the SPcode, change the line1 (javaaddpath) to the path of mij.jar you just added. Change the line2 to the file path of your local ij.jar Change the line3 to the path where you stored this code Change the line4 to your local Fiji/ImageJ.app path

Once the above settings are adjusted, please change the line5 D to the folder containing raw data. line 71 to line 79 is for drift correction (Mean-shift algorithm) line 23 to line 28 is for peaking fitting (ThunderSTORM)

  1. F. J. Fazekas, T. R. Shaw, S. Kim, R. A. Bogucki, S. L. Veatch, A mean shift algorithm for drift correction in localization microscopy. Biophysical Reports. 1, 100008 (2021).
  2. M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, G. M. Hagen, ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics. 30, 2389–2390 (2014).
  3. D. Legland, I. Arganda-Carreras, P. Andrey, MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics. 32, 3532–3534 (2016).