Visualizing minute details in light-sheet and confocal microscopy data by combining 3D rolling ball filtering and deconvolution.
bioimaging
confocal microscopy
deconvolution
image processing
light-sheet microscopy
microscopy
Journal
Journal of biophotonics
ISSN: 1864-0648
Titre abrégé: J Biophotonics
Pays: Germany
ID NLM: 101318567
Informations de publication
Date de publication:
02 2022
02 2022
Historique:
revised:
27
10
2021
received:
14
09
2021
accepted:
29
10
2021
pubmed:
3
11
2021
medline:
5
3
2022
entrez:
2
11
2021
Statut:
ppublish
Résumé
We developed an open-source deconvolution software that stunningly increases the visibility of minute details, as for example, neurons or nerve fibers in light-sheet microscopy or confocal microscopy data by combining rolling ball background subtraction in three directions with deconvolution using a synthetic or measured point spread function. Via automatic block-wise processing image stacks of virtually unlimited size can be deconvolved even on small computers with 8 or 16 GB RAM. By parallelization and optional GPU-acceleration, the software works with high speed: On a PC equipped with a state-of-the-art NVidia graphic board a three dimensional (3D)-stack of about 1 billion voxels can be deconvolved within 5 to 10 minutes. The implemented variation of the Richardson-Lucy deconvolution algorithm preserves the photogrammetry of the image data by using flux-preserving regularization, an approach that to our knowledge has not been applied for deconvolving microscopy data before.
Identifiants
pubmed: 34726837
doi: 10.1002/jbio.202100290
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e202100290Informations de copyright
© 2021 The Authors. Journal of Biophotonics published by Wiley-VCH GmbH.
Références
K. Chatterjee, F. W. Pratiwi, F. C. M. Wu, P. Chen, B. C. Chen, Appl. Spectrosc. 2018, 72, 1137. https://doi.org/10.1177/0003702818778851.
J. M. Girkin, M. T. Carvalho, J. Opt. (United Kingdom) 2018, 20, 53002. https://doi.org/10.1088/2040-8986/aab58a.
C. J. Engelbrecht, E. H. Stelzer, Opt. Lett. 2006, 31, 1477. https://doi.org/10.1364/OL.31.001477.
H.-U. H.-U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, K. Becker., Nat. Methods 2007, 4, 331. https://doi.org/10.1038/nmeth1036.
K. Becker, S. Saghafi, M. Pende, I. Sabdyusheva-Litschauer, C. M. Hahn, M. Foroughipour, N. Jährling, H. U. Dodt, Sci. Rep. 2019, 9, 1. https://doi.org/10.1038/s41598-019-53875-y.
D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz, R. Guiet, C. Vonesch, M. Unser, Methods 2017, 115, 28. https://doi.org/10.1016/j.ymeth.2016.12.015.
C. Quammen Clarity-A C++ open-source deconvolution software library. http://cismm.cs.unc.edu/downloads/. 2007
S. Preibisch, F. Amat, E. Stamataki, M. Sarov, R. H. Singer, E. Myers, P. Tomancak, Nat. Methods 2014, 11, 645. https://doi.org/10.1038/nmeth.2929.
M. D. Abràmoff, I. Hospitals, P. J. Magalhães, M. Abràmoff, Biophotonics Int. 2007, 11, 36.
J. Huisken, J. Swoger, S. Linkdeck, E. H. K. Stelzer, Selective Plane Illumination Microscopy. in Handbook of Biological Confocal Microscopy, 3rd ed. (Ed: J. B. Pawley), Springer, Boston, 2006, p. 672. https://doi.org/10.1007/978-0-387-45524-2.
E. Bratsolis, M. Sigelle, Astron Astrophys. 2001, 375, 1120. https://doi.org/10.1051/0004-6361.
J. B. Sibarita, Adv. Biochem. Eng. Biotechnol. 2005, 95, 201. https://doi.org/10.1007/b102215.
L. B. Lucy, Astron J. 1974, 79, 745. https://doi.org/10.1086/111605.
W. H. Richardson, J. Opt. Soc. Am. 1972, 62, 55. https://doi.org/10.1364/JOSA.62.000055.
M. Laasmaa, M. Vendelin, P. Peterson, J. Microsc. 2011, 243, 124. https://doi.org/10.1111/j.1365-2818.2011.03486.x.
N. Dey, L. Blanc-Feraud, C. Zimmer, P. Roux, Z. V. I. Kam, J. Zerubia, Microsc. Res. Tech. 2006, 266, 260. https://doi.org/10.1002/jemt.20294.
A. N. Tikhonov, A. VY, Solutions of Ill-posed Problems, Winston, Washington, 1977 https://books.google.at/books?id=ECrvAAAAMAAJ.
R. W. Cole, T. Jinadasa, C. M. Brown, Nat. Protoc. 2011, 6, 1929. https://doi.org/10.1038/nprot.2011.407.
C. Sheppard, D. Shotton, Confocal Laser Scanning Microscopy, BIOS Scientific Publishers, Chicago, 1997.
S. R. Sternberg, Computer (Long Beach Calif). 1983, 16, 22. https://doi.org/10.1109/MC.1983.1654163.
K. Becker, N. Jährling, S. Saghafi, R. Weiler, H.-U. Dodt, PLoS One 2012, 7, e33916. https://doi.org/10.1371/journal.pone.0033916.
M. Pende, K. Becker, M. Wanis, S. Saghafi, R. Kaur, C. Hahn, N. Pende, M. Foroughipour, T. Hummel, H. U. Dodt, Nat. Commun. 2018, 9, 1. https://doi.org/10.1038/s41467-018-07192-z.
C. Hahn, K. Becker, S. Saghafi, M. Pende, A. Avdibašić, M. Foroughipour, C. T. Wotjak, H. U. Dodt, J. Biophotonics 2019, 12, e201800368. https://doi.org/10.1002/jbio.201800368.
N. Jährling, K. Becker, C. Schönbauer, F. Schnorrer, H.-U. Dodt, Front. Syst. Neurosci. 2010, 4, 1. https://doi.org/10.3389/neuro.06.001.2010.
S. F. Gibson, F. Lanni, J. Opt. Soc. Am. A 1992, 9, 154. https://doi.org/10.1364/josaa.9.000154.
J. S. Lee, T. L. E. Wee, C. M. Brown, J. Biomol. Tech. 2014, 25, 31. https://doi.org/10.7171/jbt.14-2501-002.
H. Kirshner, D. Sage, M. Unser, Appl. Fluoresc. 2011, 1, 2010 http://bigwww.epfl.ch/publications/kirshner1103.pdf.