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Widefield Fluorescence Microscope point-spread function

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company name:
Praveen Pankajakshan
license: Shareware
minimum requirements: MATLAB 7.12 (2011a)
functional limitations:
Widefield Fluorescence Microscope point-spread function 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 objectivemagObj: Objective total magnificationrindexObj: Refractive index of the objective immersion mediumccdSize: Pixel dimension of the CCD (in the plane of the camera)rindex_sp: Refractive index of the specimen mediumxysize: 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 nmdxy: 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 normalization1: L-1 normalization-------------Example usage:Note that for large z sections, the algorithms speed is dependent on the 2D fFTsWithout spherical aberration, and normalized to l-infinity:Microscope objective: 63X/1.4, oil immersionCCD camera pixel size: 6.45 micronsFluorophore 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 immersionCCD camera pixel size: 6.45 micronsSpecimen immersed has a buffer index of 1.45and imaged at 15 microns in depthFluorophore 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> 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 PankajakshanCopyright (C) 2011 Praveen PankajakshanAll rights reserved.Redistribution and use in source and binary forms, with or withoutmodification, 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 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" ANDANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIEDWARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE AREDISCLAIMED. IN NO EVENT SHALL BE LIABLE FOR ANYDIRECT, 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 ANDON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THISSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.---------------
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