Robust normalization protocols for multiplexed fluorescence bioimage analysis
Author | Raza, Shan E. Ahmed |
Author | Langenkämper, Daniel |
Author | Sirinukunwattana, Korsuk |
Author | Epstein, David |
Author | Nattkemper, Tim W. |
Author | Rajpoot, Nasir M. |
Available date | 2016-10-26T07:13:06Z |
Publication Date | 2016-03-05 |
Publication Name | BioData Mining |
Identifier | http://dx.doi.org/10.1186/s13040-016-0088-2 |
Citation | Ahmed 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. |
ISSN | 1756-0381 |
Abstract | The 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. |
Sponsor | UK 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. |
Language | en |
Publisher | BioMed Central |
Subject | Multiplexed fluorescence imaging Protein signatures Toponome imaging system Normalization protocols Bioimage informatics |
Type | Article |
Issue Number | 11 |
Volume Number | 9 |
Files in this item
This item appears in the following Collection(s)
-
Computer Science & Engineering [2284 items ]