matlab实现广角荧光显微镜的点扩散函数

收录时间:2018-01-12
资源分类:Matlab 工具:MATLAB 7.12 (R2011a)

matlab实现广角荧光显微镜的点扩散函数

 

Widefield Fluorescence Microscope point-spread function

This function generate the point-spread function for a widefield microscope using a scalar diffraction-limited model (Stokseth refer to [1] and [3] below)

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Input parameters:

lambdaEx: Excitation Wavelength (in nm)

lambdaEm: Emission wavelegnth (in nm)

numAper: Numerical aperture of the objective

magObj: Objective total magnification

rindexObj: Refractive index of the objective immersion medium

ccdSize: Pixel dimension of the CCD (in the plane of the camera)

rindex_sp: Refractive index of the specimen medium

xysize: Size of the desired image (specimen view size/pixel dimension)

nslices: Number of slices desired (Depth view/Z axis sampling)

depth: depth of the specimen under the cover-slip in nm

dxy: CCD pixel size (in nm)

dz: Optical axis Z sampling or defocusing (in nm)

nor: Normalization on the PSF (default: no normalization)

0: L-infinity normalization

1: L-1 normalization

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Example usage:

Note that for large z sections, the algorithms speed is dependent on the 2D fFTs

Without spherical aberration, and normalized to l-infinity:

Microscope objective: 63X/1.4, oil immersion

CCD camera pixel size: 6.45 microns

Fluorophore is GFP and excited in blue

>> psf = wfmpsf(488, 520, 1.4, 63, 1.518, 6450, 300, 128, 64, 1.518, 0, 0);

With spherical aberration:

Microscope objective: 63X/1.4, oil immersion

CCD camera pixel size: 6.45 microns

Specimen immersed has a buffer index of 1.45

and imaged at 15 microns in depth

Fluorophore is GFP and excited in blue

>> psf = wfmpsf(488, 520, 1.2, 40, 1.33, 6450, 300, 256, 128, 1.45, 15000, 0);

To plot the PSFs:

>> load cmap_fire;

Remove any errors due to the Fourier transform

>> psf(psf<5.7e-06) = 5.7e-06;

>> figure, imagesc(maxintensityproj(log(psfl), 1)');

>> colormap(cmap_fire); colorbar;

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References:

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[1] P. A. Stokseth (1969). `Properties of a defocused optical system'. J. Opt. Soc. Am. A 59:1314?1321.

[2] P. Pankajakshan, et al. (2010). `Point-spread function model for fluorescence macroscopy imaging'. In Proc. of Asilomar Conference on Signals, Systems and Computers.

[3] P. Pankajakshan (2009). Blind Deconvolution for Confocal Laser Scanning Microscopy. Ph.D. thesis, Universite de Nice Sophia-Antipolis.

Author: Praveen Pankajakshan

Copyright (C) 2011 Praveen Pankajakshan

All rights reserved.

 

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wfmpsf.zip (87.83KB)  
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maxintensityproj.m  wfmpsf.m  ._maxintensityproj.m  ._wfmpsf.m  
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