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Robust normalization protocols for multiplexed fluorescence bioimage analysis

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Raza, Shan-e-Ahmed, Langenkämper, Daniel, Sirinukunwattana, Korsuk, Epstein, D. B. A., Nattkemper, Tim W. and Rajpoot, Nasir M. (2016) Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Mining, 9 (11). pp. 1-13. doi:10.1186/s13040-016-0088-2

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Official URL: http://dx.doi.org/10.1186/s13040-016-0088-2

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Abstract

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.

Item Type: Journal Article
Subjects: Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software
Divisions: Faculty of Science > Computer Science
Library of Congress Subject Headings (LCSH): Imaging systems in biology, Fluorescent probes
Journal or Publication Title: BioData Mining
Publisher: BioMed Central Ltd.
ISSN: 1756-0381
Official Date: 5 March 2016
Dates:
DateEvent
5 March 2016Published
2 February 2016Accepted
17 August 2015Submitted
Date of first compliant deposit: 1 April 2016
Volume: 9
Number: 11
Number of Pages: 13
Page Range: pp. 1-13
DOI: 10.1186/s13040-016-0088-2
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
Funder: Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Qatar National Research Fund (QNRF)
Grant number: BB/K018868/1 (BBSRC), NPRP 5-1345-1-228 (QNRF)

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