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Widefield Fluorescence Microscope point-spread function 1.0
File ID: 79842






Widefield Fluorescence Microscope point-spread function 1.0
Download Widefield Fluorescence Microscope point-spread function 1.0http://www.mathworks.comReport Error Link
License: Shareware
File Size: 92.2 KB
Downloads: 10
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Widefield Fluorescence Microscope point-spread function 1.0 Description
Description: This function generate the point-spread function for a widefield microscope using a scalar diffraction-limited model (Stokseth refer to [1] and [3] below)
----------------
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
-------------
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;
---------------
References:
----------
[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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the <organization> nor the
names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
---------------

License: Shareware

Related: disclaimer, notice, reproduce, Documentation, andor, Copyright, conditions, redistributions

O/S:BSD, Linux, Solaris, Mac OS X

File Size: 92.2 KB

Downloads: 10



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