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Title: Improved deconvolution of very weak confocal signals

Deconvolution is typically used to sharpen fluorescence images, but when the signal-to-noise ratio is low, the primary benefit is reduced noise and a smoother appearance of the fluorescent structures. 3D time-lapse (4D) confocal image sets can be improved by deconvolution. However, when the confocal signals are very weak, the popular Huygens deconvolution software erases fluorescent structures that are clearly visible in the raw data. We find that this problem can be avoided by prefiltering the optical sections with a Gaussian blur. Analysis of real and simulated data indicates that the Gaussian blur prefilter preserves meaningful signals while enabling removal of background noise. Here, this approach is very simple, and it allows Huygens to be used with 4D imaging conditions that minimize photodamage.
Authors:
 [1] ;  [2] ;  [2] ;  [2] ;  [3] ; ORCiD logo [1]
  1. Univ. of Chicago,Chicago, IL (United States)
  2. Univ. of Chicago, Chicago, IL (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States)
Publication Date:
Grant/Contract Number:
AC02-06CH11357
Type:
Accepted Manuscript
Journal Name:
F1000Research
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2046-1402
Publisher:
F1000Research
Research Org:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 47 OTHER INSTRUMENTATION
OSTI Identifier:
1395871

Day, Kasey J., La Riviere, Patrick J., Chandler, Talon, Bindokas, Vytas P., Ferrier, Nicola J., and Glick, Benjamin S.. Improved deconvolution of very weak confocal signals. United States: N. p., Web. doi:10.12688/f1000research.11773.2.
Day, Kasey J., La Riviere, Patrick J., Chandler, Talon, Bindokas, Vytas P., Ferrier, Nicola J., & Glick, Benjamin S.. Improved deconvolution of very weak confocal signals. United States. doi:10.12688/f1000research.11773.2.
Day, Kasey J., La Riviere, Patrick J., Chandler, Talon, Bindokas, Vytas P., Ferrier, Nicola J., and Glick, Benjamin S.. 2017. "Improved deconvolution of very weak confocal signals". United States. doi:10.12688/f1000research.11773.2. https://www.osti.gov/servlets/purl/1395871.
@article{osti_1395871,
title = {Improved deconvolution of very weak confocal signals},
author = {Day, Kasey J. and La Riviere, Patrick J. and Chandler, Talon and Bindokas, Vytas P. and Ferrier, Nicola J. and Glick, Benjamin S.},
abstractNote = {Deconvolution is typically used to sharpen fluorescence images, but when the signal-to-noise ratio is low, the primary benefit is reduced noise and a smoother appearance of the fluorescent structures. 3D time-lapse (4D) confocal image sets can be improved by deconvolution. However, when the confocal signals are very weak, the popular Huygens deconvolution software erases fluorescent structures that are clearly visible in the raw data. We find that this problem can be avoided by prefiltering the optical sections with a Gaussian blur. Analysis of real and simulated data indicates that the Gaussian blur prefilter preserves meaningful signals while enabling removal of background noise. Here, this approach is very simple, and it allows Huygens to be used with 4D imaging conditions that minimize photodamage.},
doi = {10.12688/f1000research.11773.2},
journal = {F1000Research},
number = ,
volume = 6,
place = {United States},
year = {2017},
month = {6}
}

Works referenced in this record:

Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles
journal, October 2001
  • Cheezum, Michael K.; Walker, William F.; Guilford, William H.
  • Biophysical Journal, Vol. 81, Issue 4, p. 2378-2388
  • DOI: 10.1016/S0006-3495(01)75884-5