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AuthorRaza, Shan E. Ahmed
AuthorLangenkämper, Daniel
AuthorSirinukunwattana, Korsuk
AuthorEpstein, David
AuthorNattkemper, Tim W.
AuthorRajpoot, Nasir M.
Available date2016-10-26T07:13:06Z
Publication Date2016-03-05
Publication NameBioData Mining
Identifierhttp://dx.doi.org/10.1186/s13040-016-0088-2
CitationAhmed Raza SE, Langenkämper D, Sirinukunwattana K, Epstein D, Nattkemper TW, Rajpoot NM. Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Mining. 2016;9:11.
ISSN1756-0381
URIhttp://hdl.handle.net/10576/4926
AbstractThe study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to use the standard immuno-fluorescence microscopy in a cyclic manner (Nat Biotechnol 24:1270–8, 2006; Proc Natl Acad Sci 110:11982–7, 2013). Unfortunately, these techniques suffer from variability in intensity and positioning of signals from protein markers within a run and across different runs. Therefore, it is necessary to standardize protocols for preprocessing of the multiplexed bioimaging (MBI) data from multiple runs to a comparable scale before any further analysis can be performed on the data. In this paper, we compare various normalization protocols and propose on the basis of the obtained results, a robust normalization technique that produces consistent results on the MBI data collected from different runs using the Toponome Imaging System (TIS). Normalization results produced by the proposed method on a sample TIS data set for colorectal cancer patients were ranked favorably by two pathologists and two biologists. We show that the proposed method produces higher between class Kullback-Leibler (KL) divergence and lower within class KL divergence on a distribution of cell phenotypes from colorectal cancer and histologically normal samples.
SponsorUK BBSRC and the Qatar National Research Fund (QNRF) for partially supporting this study through project grants BB/K018868/1 and NPRP 5-1345-1-228, respectively.
Languageen
PublisherBioMed Central
SubjectMultiplexed fluorescence imaging
Protein signatures
Toponome imaging system
Normalization protocols
Bioimage informatics
TitleRobust normalization protocols for multiplexed fluorescence bioimage analysis
TypeArticle
Issue Number11
Volume Number9
dc.accessType Open Access


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