• An algorithm for automated det...

Treffer: An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging.

Title:
An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging.
Authors:
Ellefsen KL; Department of Neurobiology & Behavior, University of California, Irvine, CA 92697, USA., Settle B; Department of Neurobiology & Behavior, University of California, Irvine, CA 92697, USA., Parker I; Department of Neurobiology & Behavior, University of California, Irvine, CA 92697, USA; Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA., Smith IF; Department of Neurobiology & Behavior, University of California, Irvine, CA 92697, USA. Electronic address: ismith@uci.edu.
Source:
Cell calcium [Cell Calcium] 2014 Sep; Vol. 56 (3), pp. 147-56. Date of Electronic Publication: 2014 Jun 24.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural
Language:
English
Journal Info:
Publisher: Elsevier Country of Publication: Netherlands NLM ID: 8006226 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1532-1991 (Electronic) Linking ISSN: 01434160 NLM ISO Abbreviation: Cell Calcium Subsets: MEDLINE
Imprint Name(s):
Publication: <2003->: Amsterdam : Elsevier
Original Publication: [Edinburgh, New York] Churchill Livingston
MeSH Terms:
Algorithms*, Calcium/*metabolism , Calcium Signaling/*physiology , Microscopy, Fluorescence/*methods , Neuroblastoma/*metabolism, Automation ; Fluorescence ; Humans ; Microscopy, Fluorescence/instrumentation ; Neuroblastoma/pathology ; Tumor Cells, Cultured
References:
J Biol Chem. 1998 Oct 16;273(42):27130-6. (PMID: 9765231)
Biophys J. 2008 Dec 15;95(12):6016-24. (PMID: 18835890)
Methods. 2008 Nov;46(3):143-51. (PMID: 18929663)
Science. 1993 Oct 29;262(5134):740-4. (PMID: 8235594)
Biophys J. 2006 Mar 15;90(6):2151-63. (PMID: 16387777)
Biophys J. 2012 Apr 18;102(8):1826-36. (PMID: 22768938)
J Gen Physiol. 2005 Sep;126(3):179-92. (PMID: 16103278)
Physiol Rev. 2008 Oct;88(4):1491-545. (PMID: 18923188)
J Physiol. 1995 Feb 1;482 ( Pt 3):533-53. (PMID: 7738847)
J Physiol. 1994 Apr 1;476(1):17-28. (PMID: 8046631)
Biophys J. 2007 Jun 15;92(12):4433-43. (PMID: 17369419)
Biophys J. 2014 Feb 4;106(3):566-76. (PMID: 24507597)
J Physiol. 1997 Mar 1;499 ( Pt 2):307-14. (PMID: 9080361)
Proc Biol Sci. 1991 Dec 23;246(1317):269-74. (PMID: 1686093)
EMBO J. 2001 Jan 15;20(1-2):65-76. (PMID: 11226156)
Cold Spring Harb Perspect Biol. 2010 Nov;2(11):a004051. (PMID: 20943758)
Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6404-9. (PMID: 19332787)
Cell Calcium. 2005 Apr;37(4):283-99. (PMID: 15755490)
Sci Signal. 2009 Nov 24;2(98):ra77. (PMID: 19934435)
J Gen Physiol. 2012 Mar;139(3):189-207. (PMID: 22330954)
Biophys J. 1999 Feb;76(2):606-17. (PMID: 9929467)
Biophys J. 2011 Dec 7;101(11):2638-44. (PMID: 22261051)
J Biol Chem. 1985 Mar 25;260(6):3440-50. (PMID: 3838314)
Biophys J. 2007 Jun 15;92(12):4458-65. (PMID: 17400702)
Nat Rev Mol Cell Biol. 2000 Oct;1(1):11-21. (PMID: 11413485)
Cell Calcium. 2009 Jan;45(1):65-76. (PMID: 18639334)
Am J Physiol Cell Physiol. 2012 Aug 1;303(3):C236-43. (PMID: 22538238)
Biophys J. 2004 May;86(5):3250-9. (PMID: 15111438)
Cell Calcium. 2007 Oct-Nov;42(4-5):379-87. (PMID: 17428535)
Grant Information:
R01 GM100201 United States GM NIGMS NIH HHS; R01 GM048071 United States GM NIGMS NIH HHS; R37 GM048071 United States GM NIGMS NIH HHS; R01 GM065830 United States GM NIGMS NIH HHS; GM 048071 United States GM NIGMS NIH HHS; GM 065830 United States GM NIGMS NIH HHS; GM 100201 United States GM NIGMS NIH HHS
Contributed Indexing:
Keywords: Algorithm; Automation; Calcium; Fluorescence; Imaging; Total internal reflection microscopy
Substance Nomenclature:
SY7Q814VUP (Calcium)
Entry Date(s):
Date Created: 20140723 Date Completed: 20150519 Latest Revision: 20211021
Update Code:
20250114
PubMed Central ID:
PMC4162823
DOI:
10.1016/j.ceca.2014.06.003
PMID:
25047761
Database:
MEDLINE

Weitere Informationen

Local Ca(2+) transients such as puffs and sparks form the building blocks of cellular Ca(2+) signaling in numerous cell types. They have traditionally been studied by linescan confocal microscopy, but advances in TIRF microscopy together with improved electron-multiplied CCD (EMCCD) cameras now enable rapid (>500 frames s(-1)) imaging of subcellular Ca(2+) signals with high spatial resolution in two dimensions. This approach yields vastly more information (ca. 1 Gb min(-1)) than linescan imaging, rendering visual identification and analysis of local events imaged both laborious and subject to user bias. Here we describe a routine to rapidly automate identification and analysis of local Ca(2+) events. This features an intuitive graphical user-interfaces and runs under Matlab and the open-source Python software. The underlying algorithm features spatial and temporal noise filtering to reliably detect even small events in the presence of noisy and fluctuating baselines; localizes sites of Ca(2+) release with sub-pixel resolution; facilitates user review and editing of data; and outputs time-sequences of fluorescence ratio signals for identified event sites along with Excel-compatible tables listing amplitudes and kinetics of events.
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