Condensing Raman spectrum for single-cell phenotype analysis

doi:10.1186/1471-2105-16-S18-S15

	Condensing Raman spectrum for single-cell phenotype analysis
	Sun,Shiwei 1; Wang,Xuetao 2,3; Gao,Xin 4; Ren,Lihui 2; Su,Xiaoquan 2; Bu,Dongbo 1; Ning,Kang 2,3,5
	2015-12-09
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	16 期号:Suppl 18
摘要	AbstractBackgroundIn recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman profiling is an appealing optical microscopic method to achieve this. To fully utilize Raman proling for single-cell analysis, an extensive understanding of Raman spectra is necessary to answer questions such as which filtering methodologies are effective for pre-processing of Raman spectra, what strains can be distinguished by Raman spectra, and what features serve best as Raman-based biomarkers for single-cells, etc.ResultsIn this work, we have proposed an approach called rDisc to discretize the original Raman spectrum into only a few (usually less than 20) representative peaks (Raman shifts). The approach has advantages in removing noises, and condensing the original spectrum. In particular, effective signal processing procedures were designed to eliminate noise, utilising wavelet transform denoising, baseline correction, and signal normalization. In the discretizing process, representative peaks were selected to signicantly decrease the Raman data size. More importantly, the selected peaks are chosen as suitable to serve as key biological markers to differentiate species and other cellular features. Additionally, the classication performance of discretized spectra was found to be comparable to full spectrum having more than 1000 Raman shifts. Overall, the discretized spectrum needs about 5storage space of a full spectrum and the processing speed is considerably faster. This makes rDisc clearly superior to other methods for single-cell classication.
关键词	Raman Spectrum Linear Discriminant Analysis (LDA) K Nearest Neighbor(k-NN) Discretization
DOI	10.1186/1471-2105-16-S18-S15
语种	英语
WOS记录号	BMC:10.1186/1471-2105-16-S18-S15
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4105
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Bu,Dongbo; Ning,Kang
作者单位	1.Institute of Computing Technology of the Chinese Academy of Sciences; Key Lab of Intelligent Information Processing 2.Bioinformatics Group of Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences; CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics 3.CUDA Research Centre of Qingdao 4.King Abdullah University of Science and Technology; Computational Bioscience Research Center 5.Huazhong University of Science and Technology; College of Life Science and Technology
推荐引用方式 GB/T 7714	Sun,Shiwei,Wang,Xuetao,Gao,Xin,et al. Condensing Raman spectrum for single-cell phenotype analysis[J]. BMC Bioinformatics,2015,16(Suppl 18).
APA	Sun,Shiwei.,Wang,Xuetao.,Gao,Xin.,Ren,Lihui.,Su,Xiaoquan.,...&Ning,Kang.(2015).Condensing Raman spectrum for single-cell phenotype analysis.BMC Bioinformatics,16(Suppl 18).
MLA	Sun,Shiwei,et al."Condensing Raman spectrum for single-cell phenotype analysis".BMC Bioinformatics 16.Suppl 18(2015).