An open-source deconvolution software package for 3-D quantitative fluorescence microscopy imaging

Y SUN; P DAVIS; E. A KOSMACEK; F IANZINI; M. A MACKEY

doi:10.1111/j.1365-2818.2009.03205.x

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An open-source deconvolution software package for 3-D quantitative fluorescence microscopy imaging

Journal article

Peer reviewed

An open-source deconvolution software package for 3-D quantitative fluorescence microscopy imaging

Y SUN, P DAVIS, E. A KOSMACEK, F IANZINI and M. A MACKEY

Journal of microscopy (Oxford), Vol.236(3), pp.180-193

12/2009

DOI: 10.1111/j.1365-2818.2009.03205.x

PMCID: PMC2884373

PMID: 19941558

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Abstract

Deconvolution techniques have been widely used for restoring the 3-D quantitative information of an unknown specimen observed using a wide-field fluorescence microscope. Deconv, an open-source deconvolution software package, was developed for 3-D quantitative fluorescence microscopy imaging and was released under the GNU Public License. Deconv provides numerical routines for simulation of a 3-D point spread function and deconvolution routines implemented three constrained iterative deconvolution algorithms: one based on a Poisson noise model and two others based on a Gaussian noise model. These algorithms are presented and evaluated using synthetic images and experimentally obtained microscope images, and the use of the library is explained. Deconv allows users to assess the utility of these deconvolution algorithms and to determine which are suited for a particular imaging application. The design of Deconv makes it easy for deconvolution capabilities to be incorporated into existing imaging applications.

iterative deconvolution

Deconvolution

live cell imaging

image restoration

3-D quantitative fluorescence microscopy imaging

fluorescence microscopy

Details

Title: Subtitle: An open-source deconvolution software package for 3-D quantitative fluorescence microscopy imaging
Creators: Y SUN - Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, U.S.A
P DAVIS - Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, U.S.A
E. A KOSMACEK - Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, U.S.A
F IANZINI - Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, U.S.A
M. A MACKEY - Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, U.S.A
Resource Type: Journal article
Publication Details: Journal of microscopy (Oxford), Vol.236(3), pp.180-193
DOI: 10.1111/j.1365-2818.2009.03205.x
PMID: 19941558
PMCID: PMC2884373
ISSN: 0022-2720
eISSN: 1365-2818
Language: English
Date published: 12/2009
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Radiology
Record Identifier: 9984064103502771

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