Blind source separation techniques for the decomposition of multiply labeled fluorescence images

Biophysical Journal

Volumn 96, Issue 9, 2009, Pages 3791-3800

  Neher, Richard A ^a   Mitkovski, Mišo ^b,g   Kirchhoff, Frank ^b,g   Neher, Erwin ^c,g   Theis, Fabian J ^d,e   Zeug, André ^f,g,h  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MAX PLANCK INSTITUTE OF EXPERIMENTAL MEDICINE   (Germany)

^c MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^d INSTITUTE OF EPIDEMIOLOGY   (Germany)

^e MAX PLANCK INSTITUTE FOR DYNAMICS AND SELF ORGANIZATION   (Germany)

^f UNIVERSITY OF GÖTTINGEN   (Germany)

^g Deutsche Forschungsgemeinschaft   (Germany)

^h HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENHANCED GREEN FLUORESCENT PROTEIN; ETHIDIUM BROMIDE; FLUORESCEIN ISOTHIOCYANATE; FLUORESCENT DYE; ENHANCED CYAN FLUORESCENT PROTEIN; ETHIDIUM; GREEN FLUORESCENT PROTEIN; NUCLEIC ACID; TRANSFERRIN; TUBULIN;

ALGORITHM; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DECOMPOSITION; FLUORESCENCE MICROSCOPY; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SEPARATION TECHNIQUE; SPECTRUM; ANIMAL; BRAIN; CELL STRAIN 3T3; GENETICS; HELA CELL; IMAGE PROCESSING; METABOLISM; METHODOLOGY; MICROFILAMENT; TRANSGENIC MOUSE;

ALGORITHMS; ANIMALS; BRAIN; ETHIDIUM; FLUORESCEIN-5-ISOTHIOCYANATE; FLUORESCENT DYES; GREEN FLUORESCENT PROTEINS; HELA CELLS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICE; MICE, TRANSGENIC; MICROFILAMENTS; MICROSCOPY, FLUORESCENCE; NIH 3T3 CELLS; NUCLEIC ACIDS; TRANSFERRIN; TUBULIN;

EID: 67650379017     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.10.068     Document Type: Article

References (24)

1. Giepmans, B. N. G., S. R. Adams, M. H. Ellisman, and R. Y. Tsien. 2006. The fluorescent toolbox for assessing protein location and function. Science. 3:217-224.
2. Livet, J., T. A. Weissman, H. Kang, R. W. Draft, J. Lu, et al. 2007. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 450:56-62.
3. Dickinson, M. E., G. Bearman, S. Tille, R. Lansford, and S. E. Fraser. 2001. Multi-spectral imaging and linear unmixing add a whole new dimension to laser scanning fluorescence microscopy. Biotechniques. 31:1272-1278.
4. Bastiaens, P. I., and A. Squire. 1999. Fluorescence lifetime imaging microscopy: spatial resolution of biochemical processes in the cell. Trends Cell Biol. 9:48-52.
5. Carlsson, K., N. Aslund, K. Mossberg, and J. Philip. 1994. Simultaneous confocal recording of multiple fluorescent labels with improved channel separation. J. Microsc. 176:287-299.
6. Carlsson, K., and A. Liljeborg. 1998. Simultaneous confocal lifetime imaging of multiple fluorophores using the intensity-modulated multiple-wavelength scanning (IMS) technique. J. Microsc. 191:119-127.
7. Gobinet, C., E. Perrin, and R. Huez. 2004. Application of non-negative matrix factorization to fluorescence spectroscopy. Proc. Eur. Sig. Proc. Conf. 1095.
8. Shirakawa, H., and S. Miyazaki. 2004. Blind spectral decomposition of single-cell fluorescence by parallel factor analysis. Biophys. J. 86:1739-1752.
9. Sutherland, V. L., J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, et al. 2007. Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution. J. Neurosci. Methods. 160:144-148.
10. Mansfield, J. R., K. W. Gossage, C. C. Hoyt, and R. M. Levenson. 2005. Autofluorescence removal, multiplexing, and automated analysis methods for in-vivo fluorescence imaging. J. Biomed. Opt. 10:41207.
11. Bro, R. 1997. PARAFAC. Tutorial and applications. Chemom. Intell. Lab. Syst. 38:149-171.
12. Neher, R., and E. Neher. 2004. Optimizing imaging parameters for the separation of multiple labels in a fluorescence image. J. Microsc. 213:46-62.
13. Lee, D. D., and H. S. Seung. 1999. Learning the parts of objects by non-negative matrix factorization. Nature. 401:788-791.
14. Lee, D. D., and H. S. Seung. 2000. Algorithms for non-negative matrix factorization. Proc. Neur. Inf. Proc. Syst. 13:556-562.
15. Hirrlinger, P. G., A. Scheller, C. Braun, M. Quintela-Schneider, B. Fuss, et al. 2005. Expression of reef coral fluorescent proteins in the central nervous system of transgenic mice. Mol. Cell. Neurosci. 30:291-303.
16. Jung, S., J. Aliberti, P. Graemmel, M. J. Sunshine, G. W. Kreutzberg, et al. 2000. Analysis of fractalkine receptor CX(3)CR1 function by targeted deletion and green fluorescent protein reporter gene insertion. Mol. Cell. Biol. 20:4106-4114.
17. Lepecq, J. B., and C. A. Paoletti. 1966. New fluorometric method for RNA and DNA determination. Anal. Biochem. 17:100-107.
18. Biggiogera, M., and F. F. Biggiogera. 1989. Ethidium bromide- and propidium iodide-PTA staining of nucleic acids at the electron microscopic level. J. Histochem. Cytochem. 37:1161-1166.
19. Theis, F., K. Stadlthanner, and T. Tanaka. 2005. First results on uniqueness of sparse non-negative matrix factorization. Proc. Proc. Eur. Sig. Proc. Conf.
20. Hoyer, P. 2004. Non-negative matrix factorization with sparseness constraints. J. Mach. Learn. Res. 5:1457-1469.
21. Shashua, A., and T. Hazan. 2005. Non-negative tensor factorization with applications to statistics and computer vision. Proc. 22nd Int. Conf. Machine Learning, New York. 792.
22. Schubert, W., B. Bonnekoh, A. J. Pommer, L. Philipsen, R. Bockelmann, et al. 2006. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat. Biotechnol. 24:1270-1278.
23. Zimmermann, T., J. Rietdorf, and R. Pepperkok. 2003. Spectral imaging and its application in live cell microscopy. FEBS Lett. 546:87-92.
24. Kruskal, J. B. 1977. Three-way arrays: rank and uniqueness of tri-linear decompositions, with applications to arithmetic complexity and statistics. Linear Algebra Appl. 18:95-138.