Visualization of microscopy-based spectral imaging data from multi-label tissue sections

Current Protocols in Molecular Biology

Volumn , Issue SUPPL. 84, 2008, Pages

  Mansfield, James R ^a   Hoyt, Clifford ^a   Levenson, Richard M ^a  

^a Cambridge Research & Instrumentation Inc   (United States)

Author keywords

Data visualization; Spectral imaging; Unmixing

Indexed keywords

ESTROGEN RECEPTOR; MOLECULAR MARKER; PROGESTERONE RECEPTOR; FLUORESCENT DYE;

ANTIBODY LABELING; CALCULATION; CANCER STEM CELL; ENZYME IMMUNOASSAY; FILTER; FLOW CYTOMETRY; FLUORESCENCE; HUMAN; IMAGING SYSTEM; IMMUNOHISTOCHEMISTRY; INTRADUCTAL CARCINOMA; MICROSCOPY; PRIORITY JOURNAL; PROTEIN LOCALIZATION; REVIEW; SIMULATION; SPECTROSCOPY; SYSTEMS BIOLOGY; TISSUE SECTION; ARTICLE; CELL POPULATION; FLUORESCENCE IN SITU HYBRIDIZATION; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGING; LASER SCANNING CYTOMETRY; MATHEMATICAL ANALYSIS; METHODOLOGY; SPECTRAL SENSITIVITY; SPECTROMETER; ANIMAL; FLUORESCENCE MICROSCOPY; INSTRUMENTATION; STAINING;

ANIMALS; FLUORESCENT DYES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; IMMUNOHISTOCHEMISTRY; LASER SCANNING CYTOMETRY; MICROSCOPY, FLUORESCENCE; STAINING AND LABELING;

EID: 56149112767     PISSN: 19343639     EISSN: 19343647     Source Type: Journal    
DOI: 10.1002/0471142727.mb1419s84     Document Type: Review

References (37)

1. Ailles, L.E. and Weissman, I.L. 2007. Cancer stem cells in solid tumors. Curr. Opin. Biotech. 18:460-466.
2. Bouchard, M.B., MacLaurin, S.A., Dwyer, P.J., Mansfield, J., Levenson, R., and Krucker, T. 2007. Technical considerations in longitudinal multispectral small animal molecular imaging. J. Biomed. Opt. 12:051601.
3. Dickinson, M.E., Bearman, G., Tille, S., Lansford, R., and Fraser, S.E. 2001. Multi-spectral imaging and linear unmixing add a whole newdimension to laser scanning fluorescence microscopy. Biotechniques 31:1272, 1274-6, 1278.
4. Eismann, M.T. and Hardie, R.C. 2004. Stochastic spectral unmixing with enhanced endmember class separation. Appl. Opt. 43:6596-6608.
5. Garini, Y., Young, I.T., and McNamara, G. 2006. Spectral imaging: Principles and applications. Cytometry A 69:735-747.
6. Hameed, O. and Humphrey, P.A. 2005. p63/AMACR antibody cocktail restaining of prostate needle biopsy tissues after transfer to charged slides: A viable approach in the diagnosis of small atypical foci that are lost on block sectioning. Am. J. Clin. Pathol. 124:708-715.
7. Herawi, M. and Epstein, J.I. 2007. Immunohistochemical antibody cocktail staining (p63/HMWCK/AMACR) of ductal adenocarcinoma and Gleason pattern 4 cribriform and noncribriform acinar adenocarcinomas of the prostate. Am. J. Surg. Pathol. 31:889-894.
8. Hiraoka, Y., Shimi, T., and Haraguchi, T. 2002. Multispectral imaging fluorescence microscopy for living cells. Cell Struct. Funct. 27:367-374.
9. Horn, R.A. and Johnson, C.R. 1985. Matrix Analysis. Section 2.8. Cambridge University Press, Cambridge, England.
10. Jaskolski, F., Mulle, C., and Manzoni, O.J. 2005. An automated method to quantify and visualize colocalized fluorescent signals. J. Neurosci. Methods. 146:42-49.
11. Kariya, T. and Kurata, H. 2004. Generalized Least Squares. John Wiley & Sons, Hoboken, N.J.
12. Lambros, M.B., Natrajan, R., and Reis-Filho, J.S. 2007. Chromogenic and fluorescent in situ hybridization in breast cancer. Hum. Pathol. 38:1105-1122.
13. Lawson, C. and Hanson, R. 1974. Solving Least Squares Problems. Prentice-Hall, Englewood Cliffs, N.J.
14. Levenson, R.M. and Mansfield, J.R. 2006. Spectral imaging in biology and medicine: Slices of life. Cytometry A. 69:748-758.
15. Levenson, R.M., Lynch, D.T., Kobayashi, H., Backer, J.M., and Backer, M.V. 2008. Multiplexing with multispectral imaging: From mice to microscopy. ILAR J. 49:78-88.
16. Mansfield, J.R., Gossage, K.W., and Levenson, R.M. 2005. Autofluorescence removal, multiplexing, and automated analysis methods for invivo fluorescence imaging. J. Biomed. Optics 10:41207.
17. Miao, L., Qi, H., and Szu, H. 2007. A maximum entropy approach to unsupervised mixedpixel decomposition. IEEE Trans. Image Process. 16:1008-1021.
18. Muñoz-Barrutia, A., García-Muñoz, J., Ucar, B., Fernández-García, I., and Ortiz-de-Solorzano, C. 2007. Blind spectral unmixing of M-FISH images by non-negative matrix factorization. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2007:6248-6251.
19. Neher, R. and Neher, E. 2004. Optimizing imaging parameters for the separation of multiple labels in a fluorescence image. J. Microscopy 213:46-62.
20. Petty, H.R. 2007. Fluorescence microscopy: Established and emerging methods, experimental strategies, and applications in immunology. Microsc. Res. Tech. 70:687-709.
21. Press, W.H., Flannery, B.P., Teukolsky, S.A., and Vetterling, W.T. 1992. Convolution and deconvolution using the FFT. In Numerical Recipes in FORTRAN: The Art of Scientific Computing, 2nd ed., Sect. 13.1 pp. 531-537. Cambridge University Press, Cambridge.
22. Robertson, D., Savage, K., Reis-Filho, J.S., and Isacke, C.M. 2008. Multiple immunofluorescence labelling of formalin-fixed paraffinembedded (FFPE) tissue. BMC Cell Biol. 9:13.
23. Rothmann, C., Bar-Am, I., and Malik, Z. 1998. Spectral imaging for quantitative histology and cytogenetics. Histol. Histopathol. 13:921-926.
24. Rueden, C., Eliceiri, K.W., and White, J.G. 2004. VisBio: A computational tool for visualization of multidimensional biological image data. Traffic 5:411-417.
25. Swedlow, J.R. 2007. Quantitative fluorescence microscopy and image deconvolution. Methods Cell Biol. 81:447-465.
26. Tacha, D.E. and Miller, R.T. 2004. Use of p63/P504S monoclonal antibody cocktail in immunohistochemical staining of prostate tissue. Appl. Immunohistochem. Mol. Morphol. 12:75-78.
27. van der Loos, C.M. 1999. Multiple Immunoenzyme Staining Methods. Bios Scientific Publishers, Oxford, U.K.
28. van der Loos, C.M. 2005. Multiple staining in molecular pathology. In Molecular Morphology of Human Tissues with Light Microscopy, (G.W. Hacker and R.M. Tubbs, eds.) CRC Press, Boca Raton, Fla.
29. van der Loos, C.M. 2008. Multiple immunoenzyme staining: Methods and visualizations for the observation with spectral imaging. J. Histochem. Cytochem. 56:313-328.
30. TM) for biotinylation of mouse primary antibodies, to be used in a multistep double staining method for human tissue specimens. J. Histochem. Cytochem. 48:1431-1437.
31. van der Loos, C.M., Das, P.K., and Houthoff, H.-J. 1987. An immunoenzyme triple staining method using both polyclonal and monoclonal antibodies from the same species: Application of combined direct, indirect and avidin-biotin complex (ABC) technique. J. Histochem. Cytochem. 35:1199-1204.
32. van der Loos, C.M., van Oord, J.J., Das, P.K., and Houthoff, H.-J. 1988. Use of commercially available monoclonal antibodies for immunoenzyme double staining. Histochem. J. 20:409-413.
33. van der Loos, C.M., Volkers, H.H., Rook, R., van den Berg, F.M., and Houthoff, H-J. 1989. Simultaneous application ofDNAin situ hybridization and immunohistochemistry on one tissue section. Histochem. J. 21:279-284.
34. van der Loos, C.M., Becker, A.E., and van den Oord, J.J. 1993. Practical suggestions for successful immunoenzyme double-staining experiments. Histochem. J. 25:1-13.
35. van der Loos, C.M., Naruko, T., and Becker, A.E. 1996. The use of enhanced polymer one-step reagents for immunoenzyme double-labelling. Histochem. J. 28:709-714.
36. Zimmermann, T. 2005. Spectral imaging and linear unmixing in light microscopy. Adv. Biochem. Eng. Biotechnol. 95:245-265.
37. Zimmermann, T., Rietdorf, J., and Pepperkok, R. 2003. Spectral imaging and its applications in live cell microscopy. FEBS Lett. 546:87-92.