Preprocessing strategies to improve MCR analyses of hyperspectral images

Chemometrics and Intelligent Laboratory Systems

Volumn 117, Issue , 2012, Pages 149-158

  Jones, Howland D T ^a   Haaland, David M ^a   Sinclair, Michael B ^a   Melgaard, David K ^a   Collins, Aaron M ^a   Timlin, Jerilyn A ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

Hyperspectral imaging; Image data preprocessing; MCR; Multivariate analysis; Multivariate curve resolution; Spectral imaging

Indexed keywords

GREEN FLUORESCENT PROTEIN;

ARTICLE; AUTOMATION; CHLORELLA; FLUORESCENCE MICROSCOPY; HYPERSPECTRAL IMAGING; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGING SYSTEM; MACROPHAGE; MULTIVARIATE ANALYSIS; MULTIVARIATE CURVE RESOLUTION; NONHUMAN; PRIORITY JOURNAL; SIGNAL NOISE RATIO; SIMULATION; STATISTICAL MODEL;

EID: 84864307807     PISSN: 01697439     EISSN: 18733239     Source Type: Journal    
DOI: 10.1016/j.chemolab.2012.01.011     Document Type: Article

References (36)

1. Zimmerman T., Rietdorf J., Pepperkok R. Spectral imaging and its applications in live cell microscopy. Federation of European Biochemical Societies Letters 2003, 546:87-92.
2. Farkas D.L., Becker D. Applications of spectral imaging: detection and analysis of human melanoma and its precursors. Pigment Cell Research 2001, 14:2-8.
3. Gendrin C., Roggo Y., Collet C. Pharmaceutical applications of vibrational chemical imaging and chemometrics: a review. Journal of Pharmaceutical and Biomedical Analysis 2008, 48:533-553.
4. de Juan A., Tauler R., Dyson R., Marcolli C., Rault M., Maeder M. Spectroscopic imaging and chemometrics: a powerful combination for global and local sample analysis. TRAC Trends in Analytical Chemistry 2004, 23:70-79.
5. Widjaja E., Crane N., Chen T.-c., Morris M.D., Ignelzi M.A., McCreadie B.R. Band-target entropy minimazation (BTEM) applied to hyperspectral Raman image data. Applied Spectroscopy 2003, 57:1353-1362.
6. Tyler B.J., Rayal G., Castner D.G. Multivariate analysis strategies for processing ToF-SIMS images of biomaterials. Biomaterials 2007, 28:2412-2423.
7. Xiaobo Z., Jiewen Z., Holmes M., Hanpin M., Jiyong S., Xiaopin Y., Yanxiao L. Independent component analysis in information extraction from visible/near-infrared hyperspectral imaging data of cucumber leaves. Chemometrics and Intelligent Laboratory Systems 2010, 104:265-270.
8. Jaumot J., Gargallo R., de Juan A., Tauler R. A graphical user-friendly interface for MCR-ALS: a new tool for multivariate curve resolution in MATLAB. Chemometrics and Intelligent Laboratory Systems 2005, 76:101-110.
9. Collins A.M., Jones H.D.T., Han D., Hu Q., Beechem T.E., Timlin J.A. Carotenoid distribution in living cells of Haematococcus pluvialis (Chlorophyceae). PLoS One 2011, 6:e24302.
10. Vermaas W.F.J., Timlin J.A., Jones H.D.T., Sinclair M.B., Nieman L.T., Hamad S., Melgaard D.L., Haaland D.M. In vivo hyperspectral confocal fluorescence imaging to determine pigment localization and distribution in cyanobacterial cells. Proceedings of the National Academy of Sciences 2008, 105:4050-4055.
11. Schoonover J.R., Marx R., Zhang S.L. Multivariate curve resolution in the analysis of vibrational spectroscopy data files. Applied Spectroscopy 2003, 57:154A-170A.
12. Behrend C.J., Tarnowski C.P., Morris M.D. Identification of outliers in hyperspectral raman image data by nearest neighbor comparison. Applied Spectroscopy 2002, 56:1458-1461.
13. Zhang D., Ben-Amotz D. Removal of cosmic spikes from hyper-spectral images using a hybrid upper-bound spectrum method. Applied Spectroscopy 2002, 56:91-98.
14. Zhang D., Hanna J.D., Ben-Amotz D. Single scan cosmic spike removal using the upper bound spectrum method. Applied Spectroscopy 2003, 57:1303-1305.
15. Zhang L., Henson M.J. A practical algorithm to remove cosmic spikes in Raman imaging data for pharmaceutical applications. Applied Spectroscopy 2007, 61:1015-1020.
16. Watson D.A., Brown L.O., Gaskill D.F., Naivar M., Graves S.W., Doorn S.K., Nolan J.P. A flow cytometer for the measurement of Raman spectra. Cytometry. Part A 2008, 73A:119-128.
17. Hamilton J.C., Gemperline P.J. Mixture analysis using factor analysis. II: Self-modeling curve resolution. Journal of Chemometrics 1990, 4:1-13.
18. Jones H.D.T., Haaland D.M., Sinclair M.B., Melgaard D.K., Van Benthem M.H., Pedroso M.C. Weighting hyperspectral image data for improved multivariate curve resolution results. Journal of Chemometrics 2008, 22:482-490.
19. Blanchet L., Réhault J., Ruckebusch C., Huvenne J.P., Tauler R., de Juan A. Chemometrics description of measurement error structure: Study of an ultrafast absorption spectroscopy experiment. Analytica Chimica Acta 2009, 642:19-26.
20. Leger M.N., Vega-Montoto L., Wentzell P.D. Methods for systematic investigation of measurement error covariance matrices. Chemometrics and Intelligent Laboratory Systems 2005, 77:181-205.
21. Salmon E.D., Shaw S.L., Waters J., Waterman-Storer C.M., Maddox P.S., Yeh E., Bloom K. Chapter 10 A High-Resolution Multimode Digital Microscope System. Methods in Cell Biology 1998, 185-215. Academic Press. S. Greenfield, E.W. David (Eds.).
22. Kotula P.G., Keenan M.R., Michael J.R. Automated analysis of SEM X-Ray spectral images: a powerful new microanalysis tool. Microscopy and Microanalysis 2003, 9:1-17.
23. Budevska B.O., Sum S.T., Jones T.J. Application of Multivariate Curve Resolution for Analysis of FT-IR Microspectroscopic Images of in Situ Plant Tissue. Applied Spectroscopy 2003, 57:124-131.
24. Ohlhausen J.A.T., Keenan M.R., Kotula P.G., Peebles D.E. Multivariate statistical analysis of time-of-flight secondary ions mass spectrometry images using AXSIA. Applied Surface Science 2004, 231/232:230-234.
25. Keenan M.R., Kotula P.G. Optimal scaling of TOF-SIMS spectrum-images prior to multivariate statistical analysis. Applied Surface Science 2004, 231/232:240-244.
26. Windig W., Hornak J.P., Antalek B. Multivariate Image Analysis of Magnetic Resonance Images with the Direct Exponential Curve Resolution Algorithm (DECRA): Part 1: Algorithm and Model Study. Journal of Magnetic Resonance 1998, 132:298-306.
27. Sinclair M.B., Haaland D.M., Timlin J.A., Jones H.D.T. Hyperspectral confocal microscope. Applied Optics 2006, 45:6283-6291.
28. Haaland D.M., Jones H.D.T., Van Benthem M.H., Sinclair M.B., Melgaard D.K., Stork C.L., Pedroso M.C., Liu P., Brasier A.R., Andrews N.L., Lidke D.S. Hyperspectral Confocal Fluorescence Imaging: Exploring Alternative Multivariate Curve Resolution Approaches. Applied Spectroscopy 2009, 63:271-279.
29. Van Benthem M.H., Keenan M.R. Fast algorithm for the solution of large-scale non-negativity-constrained least squares problems. Journal of Chemometrics 2004, 18:441-450.
30. Van Benthem M.H., Keenan M.R., Haaland D.M. Application of equality constraints on variables during alternating least squares procedures. Journal of Chemometrics 2002, 16:613-622.
31. Cattell R.B. The Scree Test For The Number Of Factors. Multivariate Behavioral Research 1966, 1:245-276.
32. Haaland D.M., Thomas E.V. Partial Least-Squares Methods for Spectral Analyses 1: Relation to Other Quantitative Calibration Methods and the Extraction of Qualitative Information. Analytical Chemistry 1988, 60:1193-1202.
33. Van Etten J.L., Burbank D.E., Xia Y., Meints R.H. Growth cycle of a virus, PBCV-1, that infects Chlorella-like algae. Virology 1983, 126:117-125.
34. Keenan M.R., Kotula P.G. Accounting for Poisson noise in the multivariate analysis of ToF-SIMS spectrum images. Surface and Interface Analysis 2004, 36:203-212.
35. Windig W., Keenan M.R., Wise B.M. The effects of pre-processing of image data on self-modeling image analysis. Journal of Chemometrics 2008, 22:500-509.
36. Haaland D.M., Easterling R.G., Vopicka D.A. Multivariate Least-Squares Methods Applied to the Quantitative Spectral-Analysis of Multicomponent Samples. Applied Spectroscopy 1985, 39:73-83.