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The Collection, Processing, and Display of Digital Three-Dimensional Images of Biological Specimens

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Handbook of Biological Confocal Microscopy

Abstract

In general, the study and analysis of biological structure requires a three-dimensional (3D) imaging capability. Dramatic technical advances have now made it possible to record 3D microscopic images of biological specimens using either electron or light microscopy. While the collection of 3D data sets has now become routine, the analysis and interpretation of these images generally require significant time and effort. This is true, in part, because each type of image seems to require a specific set of processing algorithms and parameters. In addition, the software tools required for extracting useful information from the resulting complicated multidimensional data sets (e.g., three spatial dimensions, time, different components) are not completely developed. Computational image processing provides a powerful approach for reducing the systematic errors present in any 3D data set and enhancing the clarity and contrast of relevant features.

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References

  • Agard, D.A., Hiraoka, Y., Shaw, P., and Sedat, J.W., 1989, Fluorescence microscopy in three dimensions, Methods Cell Biol. 30:353–377.

    Article  PubMed  CAS  Google Scholar 

  • Aikens, R.S., Agard, D.A., and Sedat, J.W., 1989, Solid-state imagers for microscopy, Methods Cell Biol. 29:291–313.

    Article  PubMed  CAS  Google Scholar 

  • Andrews, H.C., Tescher, A.G., and Kruger, R.P., 1972, Image processing by digital computer, IEEE Spect. 9:20–32.

    Article  Google Scholar 

  • Bui-Tuong, P., 1975, Illumination for computer generated pictures, CACM June:311–317.

    Google Scholar 

  • Castleman, K.R., 1979, Digital Image Processing, Prentice-Hall, Englewood Cliffs, New Jersey.

    Google Scholar 

  • Cline, H.E., Lorensen, W.E., Ludke, S., Crawford, C.R., and Teeter, B.C., 1988, Two algorithms for the three-dimensional reconstruction of tomograms, Med. Phys. 15:320–327.

    Article  PubMed  CAS  Google Scholar 

  • Dreibin, R.A., Carpenter, L., and Hanranhan, P., 1988, Volume rendering, Computer Graphics 22:65–75.

    Article  Google Scholar 

  • Gibson, S.F., and Lanni, F., 1991, Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy, J. Opt. Soc. Am. 8:1601–1613.

    Article  CAS  Google Scholar 

  • Giloh, H., and Sedat, J.W., 1982, Fluorescence microscopy: Reduced pho-tobleaching of rhodamine and fluorescein protein conjugates by n-propyl gallate, Science 217:1252–1255.

    Article  PubMed  CAS  Google Scholar 

  • Hell, S., Reiner, G., Cremer, C., and Stelzer, E.H.K., 1993, Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index, J. Microsc. 169:391–405.

    Article  Google Scholar 

  • Highett, M.I., Beven, A.F., and Shaw, P.J., 1993, Localization of 5 S genes and transcripts in Pisum sativum nuclei, J. Cell Sci. 105:1151–1158.

    PubMed  CAS  Google Scholar 

  • Hiraoka, Y., Sedat, J., and Agard, D., 1987, The use of a charge coupled device for quantitative optical microscopy of biological structures, Science 238:36–41.

    Article  PubMed  CAS  Google Scholar 

  • Hiraoka, Y., Minden, J.S., Swedlow, J.R., Sedat, J.W., and Agard, D.A., 1989, Focal points for chromosome condensation and decondensation revealed by three-dimensional in vivo time-lapse microscopy, Nature 342:293–296.

    Article  PubMed  CAS  Google Scholar 

  • Hiraoka, Y., Sedat, J.W., and Agard, D.A., 1990, Determination of three-dimensional imaging properties of a light microscope system, Biophys. J. 57:325–333.

    Article  PubMed  CAS  Google Scholar 

  • Hiraoka, Y., Swedlow, J.R., Paddy, M.R., Agard, D.A., and Sedat, J.W., 1991, Three-dimensional multiple-wavelength fluorescence microscopy for the structural analysis of biological phenomena, Semin. Cell Biol. 2:153–165.

    PubMed  CAS  Google Scholar 

  • Huang, T.S., Yang, G.J., and Tang, G.Y., 1979, A fast two-dimensional median filtering algorithm, IEEE Trans. Acoust. Speech Sig. Proc. 27:13–18.

    Article  Google Scholar 

  • Kam, Z., Jones, M.O., Chen, H., Agard, D.A., and Sedat, J.W., 1993, Design and construction of an optimal illumination system for quantitative wide-field multi-dimensional microscopy, Bioimaging 1:71–81.

    Article  Google Scholar 

  • Kaufman, A., 1991, Volume Visualization, IEEE Computer Society Press, Los Alamitos, California.

    Google Scholar 

  • Narendra, P.M., 1981, A separable median filter for image noise smoothing, IEEE Trans. Pat. Anal. Mach. Intel. 3:20–29.

    Article  CAS  Google Scholar 

  • Neider, J.A., and Mead, R., 1965, A simplex method for function minimization, Computer J. 7:308–313.

    Article  Google Scholar 

  • Parkinson, J.M., and Hutchison, D., 1972, An investigation into the efficiency of variants of the simplex method. In: Numerical Methods for Nonlinear Optimization, Academic Press, London.

    Google Scholar 

  • Pawley, J.B., 1994, The sources of noise in three-dimensional microscopical data sets. In: Three Dimensional Confocal Microscopy: Volume Investigation of Biological Specimens (J. Stevens, ed.), Academic Press, San Diego, pp. 47–94.

    Chapter  Google Scholar 

  • Pratt, W.K., 1978, Digital Image Processing, John Wiley &; Sons, New York.

    Google Scholar 

  • Russ, J.C., 1992, The Image Processing Handbook, CRC Press, Boca Raton, Florida.

    Google Scholar 

  • Shaw, P.J., Agard, D.A., Hiraoka, Y., and Sedat, J.W., 1989, Tilted view reconstruction in optical microscopy. Three-dimensional reconstruction of Drosophila melanogaster embryo nuclei, Biophys. J. 55:101–110.

    CAS  Google Scholar 

  • Sullivan, W., Minden, J.S., and Alberts, B.M., 1990, daugtherless abo-like, a Drosophila maternal-effect mutation that exhibits abnormal centrosome separation during the late blastoderm divisons, Development 110:311–323.

    PubMed  CAS  Google Scholar 

  • Swedlow, J.R., Sedat, J.W., and Agard, D.A., 1993, Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide field microscopy, Cell 73:97–108.

    Article  PubMed  CAS  Google Scholar 

  • Tsien, R.Y., and Waggoner, A., 1990, Fluorophores for confocal microscopy: Photophysics and photochemistry. In: Handbook of Biological Confocal Microscopy (J.B. Pawley, ed.), Plenum Press, New York, pp. 169–178.

    Chapter  Google Scholar 

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Chen, H., Swedlow, J.R., Grote, M., Sedat, J.W., Agard, D.A. (1995). The Collection, Processing, and Display of Digital Three-Dimensional Images of Biological Specimens. In: Pawley, J.B. (eds) Handbook of Biological Confocal Microscopy. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-5348-6_13

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  • DOI: https://doi.org/10.1007/978-1-4757-5348-6_13

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4757-5350-9

  • Online ISBN: 978-1-4757-5348-6

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