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Showing content from https://github.com/MicroscPSF/MicroscPSF-Matlab below:

MicroscPSF/MicroscPSF-Matlab: Fast and Accurate 3D PSF Computation for Fluorescence Microscopy

J. Li, F. Xue and T. Blu, J. Opt. Soc. Am. A, 34(6), pp. 1029-1034, 2017.

This set of codes is a fast approximation of 3D PSF model in fluorescernce microscopy, based on Gibson-Lanni model. See the page for details.

Fast approximation Current approximation can be 498 times faster than the state-of-the-art tool PSF Generator for size 511x511x255. Note the PSF Generator uses Java language with mult-threading, while the proposed uses pure Matlab without any compiled routine.

If the parameters of the microscope are not assigned, default setting will be loaded, see MicroscPSF for details.

params.size = [256 256 128];
tic;
PSF = MicroPSF(params);
toc

The last interpolation step is implementated using mex files, which reduce the time cost 50%.

cd Utilities
mex transformation.cpp

params.size = [256 256 128];
params.fastcom = 1;
tic;
PSF = MicroPSF(params);
toc

• (04 May, 2017) Add mex implementation, the speed is further improved 2 times!
• (28 Dec, 2016) Refined basis functions.
• (09 Oct, 2016) Optimized code, the speed has been improved 10 times faster!

• Matlab code: https://github.com/hijizhou/MicroscPSF-Matlab.

• ImageJ plugin: https://github.com/hijizhou/MicroscPSF-ImageJ.

• Icy plugin: https://github.com/hijizhou/MicroscPSF-Icy.

• Python code (by Dr. Kyle Douglass): http://kmdouglass.github.io/posts/implementing-a-fast-gibson-lanni-psf-solver-in-python.html

PSFgenerator

Copyright (c) 2017, Jizhou Li, Feng Xue and Thierry Blu

The source code is released under the MIT license.

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