Three‐Dimensional Image Visualization and Analysis

Stephen J. Lockett1

1 Lawrence Berkeley National Laboratory, Berkeley, California
Publication Name:  Current Protocols in Cytometry
Unit Number:  Unit 10.10
DOI:  10.1002/0471142956.cy1010s10
Online Posting Date:  May, 2001
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This unit introduces the concepts of 3D image analysis and visualization as applied in cytometry. The author discusses the nature of 3D data sets and describes the techniques for visualization and analysis of 3D images. Discussions of noise removal, depth attenuation, and correction and segmentation are also included, as is a brief introduction to 3D analysis options and deconvolution prinicples. This commentary unit is a good way to begin an understanding of the application of 3D data sets.

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Table of Contents

  • Definitions
  • Description of a 3D Image
  • Display of 3D Images
  • Volume Rendering
  • Surface Rendering
  • 3D Image Analysis
  • Neighborhood of a Voxel
  • Noise‐Removal Method for 3D Fluorescence Images
  • Depth Attenuation and Correction
  • Example of Segmentation of a 3D Confocal Microscope Image
  • Measurement of 3D Objects
  • Deconvolution of 3D Images Acquired Using Conventional Epifluorescence Microscopy
  • 3D Reconstruction of Tissue from Serial Thin Sections
  • Other Forms of 3D Imaging
  • Examples of 3D Image Analysis in Cytometry
  • Literature Cited
  • Figures
  • Tables
PDF or HTML at Wiley Online Library


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Literature Cited

   Agard, D.A., Hiraoka, Y., Shaw, P., and Sedat, J.W. 1989. Fluorescence microscopy in three dimensions. Methods Cell Biol. 30:353‐77.
   Albert, R., Schindewolf, T., Baumann, I., and Harms, H. 1992. Three‐dimensional image processing for morphometric analysis of epithelium sections. Cytometry 13:759‐765.
   Camacho, P. and Lechleiter, J.D. 1993. Increased frequency of Ca2+ waves in Xenopus laevis oocytes expressing a Ca2+‐ATPase. Science 260:226‐229.
   Carlbom, I., Terzopoulos, D., and Harris, K.M. 1994. Computer‐assisted registration, segmentation, and 3D reconstruction from images of neuronal tissue sections. IEEE Trans. Med. Image. 13:351‐362.
   Castleman, K.R. 1996. Digital Image Processing. Prentice Hall, Englewood Cliffs, N.J.
   Cremer, C., Münkel, C., Granzow, M., Jauch, A., Dietzel, S., Eils, R., Guan, X.Y., Meltzer, P.S., Trent, J.M., Langowski, J., and Cremer, T. 1996. Nuclear architecture and the induction of chromosomal aberrations. Mutation Res. 366:97‐116.
   Höfers, C., Baumann, P., Hummer, G., Jovin, T.M., and Arndt‐Jovin, D.J. 1993. The localization of chromosome domains in human interphase nuclei: Three‐dimensional distance determinations of fluorescence in situ hybridization signals from confocal laser scanning microscopy. Bioimaging 1:96‐106.
   Inoué, S. and Spring, K.R. 1997. Video Microscopy. Plenum, London.
   Kaufman, M.H., Brune, R.M., Davidson, D.R., and Baldock, R.A. 1998. Computer‐generated three‐dimensional reconstructions of serially sectioned mouse embryos. J. Anat. 193:323‐336.
   Kay, P.A., Robb, R.A., and Bostwick, D.G. 1998. Prostate cancer microvessels: A novel method for three‐dimensional reconstruction and analysis. Prostate 37:270‐277.
   Lockett, S.J., Sudar, D., Thompson, C.T., Pinkel, D., and Gray, J.W. 1998a. Efficient, interactive, and three dimensional segmentation of cell nuclei in thick tissue sections. Cytometry 31:275‐286.
   Lockett, S.J., Fernandez, C., Rodriguez, E., Wesselmann, U., Bastian, B.C., Sudar, D., Pinkel, D., and Gray, J.W. 1998b. Interactive system for registering adjacent tissue sections. Proc. SPIE 3260:154‐161.
   Noordmans, H.J., van der Kraan, K., van Driel, R., and Smeulders, A.W.M. 1998. Randomness of spatial distributions of two proteins in the cell nucleus involved in mRNA synthesis and their relationships. Cytometry 33:297‐309.
   Ortiz de Solorzano, C., Rodriguez, E.G., Jones, A., Sudar, D., Pinkel, D., Gray, J.W., and Lockett, S.J. 1999. Automatic nuclear segmentation for 3D thick tissue confocal microscopy. J. Microsc. 193:212‐226.
   Rigaut, J.P., Vassy, J., Herlin, P., Duigou, F., Masson, E., Briane, D., Foucrier, J., Carvajal‐Gonzalez, S., Downs, A.M., and Mandard, A.‐M. 1991. Three‐dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks. Cytometry 12:511‐524.
   Rothman, C., Bar‐Am, I., and Malik, Z. 1998. Spectral imaging for quantitative histology and cytogenetics. Histol. Histopathol. 13:921‐926.
   Thomas, C.F. and White, J.G. 1998. Four‐dimensional imaging: The exploration of space and time. Trends Biotechnol. 16:175‐182.
   Thompson, C.T., LeBoit, P.E., Nederlof, P.M., and Gray, J.W. 1994. Thick‐section fluorescence in situ hybridization on formalin‐fixed, paraffin‐embedded archival tissue provides a histogenetic profile. Am. J. Pathol. 144:237‐243.
   Verbeek, F.J. 1995. Three‐Dimensional Reconstruction of Biological Objects from Serial Sections Including Deformation Correction. Ph.D. Thesis, Technical University of Delft, The Netherlands.
   Wartenberg, M., Hescheler, J., Acker, H., Diedershagen, H., and Sauer, H. 1998. Doxorubicin distribution in multicellular prostate cancer spheroids evaluated by confocal laser scanning microscopy and the “optical probe technique.” Cytometry 31:137‐145.
   Wessels, D., Voss, E., Von Bergen, N., Burns, R., Stites, J., and Soll, D.R. 1998. A computer‐assisted system for reconstructing and interpreting the dynamic three‐dimensional relationships of the outer surface, nucleus and pseudopods of crawling cells. Cell Motil. Cytoskeleton 41:225‐246.
   Yelamarty, R.V., Miller, B.A., Scaduto, R.C., Yu, F.T.S., Tillotson, D.L., and Cheung, J.Y. 1990. Three‐dimensional intracellular calcium gradients in single human burst‐forming units‐erythroid‐derived erythroblasts induced by erythropoietin. J. Clin. Invest. 85:1799‐1809.
   Young, H.D. 1962. Statistical Treatment of Experimental Data Waveland Press Prospect Heights, IL.
Internet Resources
  The Mouse Atlas and Gene Expression Database Project.
  Comprehensive list of image processing and analysis software packages.
  Purdue University Cytometry Laboratories. Provider of the Microscopy CD‐ROM containing examples of 2D, 3D, and time‐lapse fluorescence microscope images, software, reference and educational material, and microscopy Web sites.
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