Improved deconvolution of very weak confocal signals
Abstract
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. This approach is very simple, and it allows Huygens to be used with 4D imaging conditions that minimize photodamage .
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1484822
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Published Article
- Journal Name:
- F1000Research
- Additional Journal Information:
- Journal Name: F1000Research Journal Volume: 6; Journal ID: ISSN 2046-1402
- Publisher:
- F1000 Research, Ltd.
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Day, Kasey J., La Rivière, Patrick J., Chandler, Talon, Bindokas, Vytas P., Ferrier, Nicola J., and Glick, Benjamin S. Improved deconvolution of very weak confocal signals. United Kingdom: N. p., 2017.
Web. doi:10.12688/f1000research.11773.1.
Day, Kasey J., La Rivière, Patrick J., Chandler, Talon, Bindokas, Vytas P., Ferrier, Nicola J., & Glick, Benjamin S. Improved deconvolution of very weak confocal signals. United Kingdom. https://doi.org/10.12688/f1000research.11773.1
Day, Kasey J., La Rivière, Patrick J., Chandler, Talon, Bindokas, Vytas P., Ferrier, Nicola J., and Glick, Benjamin S. Tue .
"Improved deconvolution of very weak confocal signals". United Kingdom. https://doi.org/10.12688/f1000research.11773.1.
@article{osti_1484822,
title = {Improved deconvolution of very weak confocal signals},
author = {Day, Kasey J. and La Rivière, 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. This approach is very simple, and it allows Huygens to be used with 4D imaging conditions that minimize photodamage .},
doi = {10.12688/f1000research.11773.1},
journal = {F1000Research},
number = ,
volume = 6,
place = {United Kingdom},
year = {Tue Jun 06 00:00:00 EDT 2017},
month = {Tue Jun 06 00:00:00 EDT 2017}
}
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https://doi.org/10.12688/f1000research.11773.1
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Works referenced in this record:
COPI selectively drives maturation of the early Golgi
journal, December 2015
- Papanikou, Effrosyni; Day, Kasey J.; Austin, Jotham
- eLife, Vol. 4
Fast live simultaneous multiwavelength four-dimensional optical microscopy
journal, August 2010
- Carlton, P. M.; Boulanger, J.; Kervrann, C.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 37
Golgi maturation visualized in living yeast
journal, May 2006
- Losev, Eugene; Reinke, Catherine A.; Jellen, Jennifer
- Nature, Vol. 441, Issue 7096
A quantitative comparison of image restoration methods for confocal microscopy
journal, March 1997
- Van Kempen, G. M. P.; Van Vliet, L. J.; Verveer, P. J.
- Journal of Microscopy, Vol. 185, Issue 3
DeconvolutionLab2: An open-source software for deconvolution microscopy
journal, February 2017
- Sage, Daniel; Donati, Lauréne; Soulez, Ferréol
- Methods, Vol. 115
Different subcellular localization of Saccharomyces cerevisiae HMG-CoA reductase isozymes at elevated levels corresponds to distinct endoplasmic reticulum membrane proliferations.
journal, May 1996
- Koning, A. J.; Roberts, C. J.; Wright, R. L.
- Molecular Biology of the Cell, Vol. 7, Issue 5
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
De novo formation of transitional ER sites and Golgi structures in Pichia pastoris
journal, September 2002
- Bevis, Brooke J.; Hammond, Adam T.; Reinke, Catherine A.
- Nature Cell Biology, Vol. 4, Issue 10
High-resolution restoration of 3D structures from widefield images with extreme low signal-to-noise-ratio
journal, October 2013
- Arigovindan, M.; Fung, J. C.; Elnatan, D.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 43
TIFF files for the experimental and simulated image data are provided in the compressed folder Original Image Files.zip.
dataset, January 2017
- Day, Kasey J.; Rivière, Patrick J. La; Chandler, Talon
- F1000Research
3D Deconvolution Microscopy
journal, April 2010
- Biggs, David S. C.
- Current Protocols in Cytometry, Vol. 52, Issue 1
Raising the Speed Limits for 4D Fluorescence Microscopy: Raising the Speed Limits
journal, December 2000
- Hammond, Adam T.; Glick, Benjamin S.
- Traffic, Vol. 1, Issue 12