Use of multiple singular value decompositions to analyze complex intracellular calcium ion signals

Handle URI:
http://hdl.handle.net/10754/600144
Title:
Use of multiple singular value decompositions to analyze complex intracellular calcium ion signals
Authors:
Martinez, Josue G.; Huang, Jianhua Z.; Burghardt, Robert C.; Barhoumi, Rola; Carroll, Raymond J.
Abstract:
We compare calcium ion signaling (Ca(2+)) between two exposures; the data are present as movies, or, more prosaically, time series of images. This paper describes novel uses of singular value decompositions (SVD) and weighted versions of them (WSVD) to extract the signals from such movies, in a way that is semi-automatic and tuned closely to the actual data and their many complexities. These complexities include the following. First, the images themselves are of no interest: all interest focuses on the behavior of individual cells across time, and thus, the cells need to be segmented in an automated manner. Second, the cells themselves have 100+ pixels, so that they form 100+ curves measured over time, so that data compression is required to extract the features of these curves. Third, some of the pixels in some of the cells are subject to image saturation due to bit depth limits, and this saturation needs to be accounted for if one is to normalize the images in a reasonably un-biased manner. Finally, the Ca(2+) signals have oscillations or waves that vary with time and these signals need to be extracted. Thus, our aim is to show how to use multiple weighted and standard singular value decompositions to detect, extract and clarify the Ca(2+) signals. Our signal extraction methods then lead to simple although finely focused statistical methods to compare Ca(2+) signals across experimental conditions.
Citation:
Martinez JG, Huang JZ, Burghardt RC, Barhoumi R, Carroll RJ (2009) Use of multiple singular value decompositions to analyze complex intracellular calcium ion signals. The Annals of Applied Statistics 3: 1467–1492. Available: http://dx.doi.org/10.1214/09-AOAS253.
Publisher:
Institute of Mathematical Statistics
Journal:
The Annals of Applied Statistics
KAUST Grant Number:
KUS-CI-016-04
Issue Date:
Dec-2009
DOI:
10.1214/09-AOAS253
PubMed ID:
20428493
PubMed Central ID:
PMC2859732
Type:
Article
ISSN:
1932-6157
Sponsors:
Supported by a postdoctoral training grant from the National Cancer Institute (CA90301).Supported by a grant from the National Cancer Institute (CA57030) and by Award Number KUS-CI-016-04, made by King Abdullah University of Science and Technology (KAUST).Supported by a grant from the National Science Foundation (DMS-06-06580).Calcium imaging performed in the College of Veterinary Medicine & Biomedical Sciences Image Analysis Laboratory, was supported by NIH-NIEHS Grants P30-ES09106, P42-ES04917 and T32 ES07273.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMartinez, Josue G.en
dc.contributor.authorHuang, Jianhua Z.en
dc.contributor.authorBurghardt, Robert C.en
dc.contributor.authorBarhoumi, Rolaen
dc.contributor.authorCarroll, Raymond J.en
dc.date.accessioned2016-02-28T06:43:38Zen
dc.date.available2016-02-28T06:43:38Zen
dc.date.issued2009-12en
dc.identifier.citationMartinez JG, Huang JZ, Burghardt RC, Barhoumi R, Carroll RJ (2009) Use of multiple singular value decompositions to analyze complex intracellular calcium ion signals. The Annals of Applied Statistics 3: 1467–1492. Available: http://dx.doi.org/10.1214/09-AOAS253.en
dc.identifier.issn1932-6157en
dc.identifier.pmid20428493en
dc.identifier.doi10.1214/09-AOAS253en
dc.identifier.urihttp://hdl.handle.net/10754/600144en
dc.description.abstractWe compare calcium ion signaling (Ca(2+)) between two exposures; the data are present as movies, or, more prosaically, time series of images. This paper describes novel uses of singular value decompositions (SVD) and weighted versions of them (WSVD) to extract the signals from such movies, in a way that is semi-automatic and tuned closely to the actual data and their many complexities. These complexities include the following. First, the images themselves are of no interest: all interest focuses on the behavior of individual cells across time, and thus, the cells need to be segmented in an automated manner. Second, the cells themselves have 100+ pixels, so that they form 100+ curves measured over time, so that data compression is required to extract the features of these curves. Third, some of the pixels in some of the cells are subject to image saturation due to bit depth limits, and this saturation needs to be accounted for if one is to normalize the images in a reasonably un-biased manner. Finally, the Ca(2+) signals have oscillations or waves that vary with time and these signals need to be extracted. Thus, our aim is to show how to use multiple weighted and standard singular value decompositions to detect, extract and clarify the Ca(2+) signals. Our signal extraction methods then lead to simple although finely focused statistical methods to compare Ca(2+) signals across experimental conditions.en
dc.description.sponsorshipSupported by a postdoctoral training grant from the National Cancer Institute (CA90301).Supported by a grant from the National Cancer Institute (CA57030) and by Award Number KUS-CI-016-04, made by King Abdullah University of Science and Technology (KAUST).Supported by a grant from the National Science Foundation (DMS-06-06580).Calcium imaging performed in the College of Veterinary Medicine & Biomedical Sciences Image Analysis Laboratory, was supported by NIH-NIEHS Grants P30-ES09106, P42-ES04917 and T32 ES07273.en
dc.publisherInstitute of Mathematical Statisticsen
dc.titleUse of multiple singular value decompositions to analyze complex intracellular calcium ion signalsen
dc.typeArticleen
dc.identifier.journalThe Annals of Applied Statisticsen
dc.identifier.pmcidPMC2859732en
dc.contributor.institutionDepartment of Statistics, Texas A&M University, 3143 Tamu, College Station, Texas 77843-3143, USA.en
kaust.grant.numberKUS-CI-016-04en

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