Abstract
The ability of confocal laser-scanning microscopy to collect stacks of optical sections has made three-dimensional (volumetric) imaging a standard analytical tool in experimental cell and developmental biology. Parallel developments in deconvolution techniques, especially as computational power increased and costs decreased, offered tools to make three-dimensional (3D) imaging from widefield as well as confocal microscopes possible. Despite the high spatial resolution provided by these 3D methods, they all suffer from a common limitation: light scattering in the specimen limits them to operating in the outer few hundred micrometers of the specimen.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Allen, M.J., and Meade, T.J., 2004, Magnetic resonance contrast agents for medical and molecular imaging. Met. Ions. Biol. Syst. 42:1–38.
Aoki, I., Wu, Y.J., Silva, A.C., Lynch, R.M., and Koretsky, A.P., 2004, In vivo detection of neuroarchitecture in the rodent brain using manganeseenhanced MRI, Neuroimage 22:1046–1059.
As, H.V., and Lens, P., 2001, Use of 1H NMR to study transport processes in porous biosystems, J. Ind. Microbiol. Biotechnol. 26:43–52.
Bock, N.A., Konyer, N.B., and Henkelman, R.M., 2003, Multiple-mouse MRI, Magn. Reson. Med. 49:158–167.
Boppart, S.A., Bouma, B.E., Pitris, C., Southern, J.F., Brezinski, M.E., and Fujimoto, J.G., 1998, In vivo cellular optical coherence tomography imaging, Nat. Med. 4:861–865.
Boppart, S.A., Brezinski, M.E., Bouma, B.E., Tearney, G.J., and Fujimoto, J.G., 1996, Investigation of developing embryonic morphology using optical coherence tomography, Dev. Biol. 177:54–63.
Boppart, S.A., Tearney, G.J., Bouma, B.E., Southern, J.F., Brezinski, M.E., and Fujimoto, J.G., 1997, Noninvasive assessment of the developing Xenopus cardiovascular system using optical coherence tomography, Proc. Natl. Acad. Sci. USA 94:4256–4261.
Callaghan, P.T., 1991, Principles of Nuclear Magnetic Resonance Microscopy, Oxford University Press, Oxford, United Kingdom.
Chapon, C., Franconi, F., Roux, J., Marescaux, L., Le Jeune, J.J., and Lemaire, L., 2002, In utero time-course assessment of mouse embryo development using high resolution magnetic resonance imaging, Anat. Embryol. 206(1–2):131–137.
Ciobanu, L., and Pennington, C.H., 2004, 3D micron-scale MRI of single biological cells, Solid State Nucl. Magn. Reson. 25:138–141.
Dhenain, M., Ruffins, S.W., and Jacobs, R.E., 2001, Three-dimensional digital mouse atlas using high-resolution MRI, Dev. Biol. 232:458–470.
Dixon, A.E., Damaskinos, S., Ribes, A., and Beesley, K.M., 1995, A new confocal scanning beam laser macroscope using a telecentric, f-theta laser scan lens, J. Microsc. 178:261–266.
Edzes, H.T., van Dusschoten, D., and Van As, H., 1998, Quantitative T2 imaging of plant tissues by means of multi-echo MRI microscopy, Magn. Reson. Imaging 16(2):185–96.
Ewald, A.J., McBride, H., Reddington, M., Fraser, S.E., and Kerschmann, R., 2002, Surface imaging microscopy, an automated method for visualizing whole embryo samples in three dimensions at high resolution, Dev. Dyn. 225:369–375.
Ewald, A.J., Peyrot, S.M., Tyszka, J.M., Fraser, S.E., and Wallingford, J.B., 2004, Regional requirements for Dishevelled signaling during Xenopus gastrulation: Separable effects on blastopore closure, mesendoderm internalization and archenteron formation, Development 131:6195–6209.
Fercher, A.F., 1996, Optical coherence tomography, J. Biomed. Opt. 1:157–173.
Foster-Gareau, P., Heyn, C., Alejski, A., and Rutt, B.K., 2003, Imaging single mammalian cells with a 1.5T clinical MRI scanner, Magn. Reson. Med. 49:968–971.
Grant, S.C., Buckley, D.L., Gibbs, S., Webb, A.G., and Blackband, S.J., 2001, MR microscopy of multicomponent diffusion in single neurons, Magn. Reson. Med. 46:1107–1112.
Haskell, R.C., Williams, M.E., Petersen, D.C., et al., 2004, Visualizing early frog development with motion-sensitive 3-D optical coherence microscopy, In: Proceedings of the 26th Annual International Conference of the IEEE EMBS, IEEE, San Francisco, CA, USA.
Herman, G.T., 1980, Image Reconstruction from Projections: The Fundamentals of Computerized Tomography, Academic Press, San Francisco.
Hinds, K.A., Hill, J.M., Shapiro, E.M., et al., 2003, Highly efficient endosomal labeling of progenitor and stem cells with large magnetic particles
allows magnetic resonance imaging of single cells, Blood 102:867–872.
Hoeling, B.M., Fernandez, A.D., Haskell, R.C., and Petersen, D.C., 2001, Phase modulation at 125 kHz in a Michelson interferometer using an inexpensive piezoelectric stack driven at resonance, Rev. Sci. Instrum. 72:1630–1633.
Hoeling, B.M., Fernandez, A.D., Haskell, R.C., Huang, E., Meyers, W.R., Petersen, D.C., Ungersma, S.E., Wang, R., and Williams, M.E., 2000, An optical coherence microscope for 3-dimensional imaging in developmental biology, Opt. Express 6:136–146.
Holdsworth, D.W., and Thornton, M.M., 2002, MicroCT in small animal and specimen imaging, Trends Biotechnol. 20(Suppl.):S34–S39.
Huang, D., Swanson, E.A., Lin, C.P., Schuman, J.S., Stinson, W.G., Chang, W.,
Hee, M.R., Flotte, T., Gregory, K., Puliafito, C.A., Fujimoto, J.G., 1991, Opt. Coherence Tomogr. Sci. 254:1178–1181.
Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J., and Stelzer, E.H.K., 2004, Optical sectioning deep inside live embryos by selective plane illumination microscopy, Science 305:1007–1009.
Izatt, J.A., Kulkarni, M.D., Wang, H.-W., Kobayashi, K., and Sivak, M.V. Jr., 1996, Optical coherence tomography and microscopy in gastrointestinal tissues, IEEE J. Sel. Topics Quant. Electron. 2:1017–1028.
Jacobs, R.E., Ahrens, E.T., Dickinson, M.E., and Laidlaw, D., 1999, Towards a microMRI atlas of mouse development, Comput. Med. Imaging Graph.23(1):15–24.
Jacobs, R.E., Papan, C., Ruffins, S., Tyszka, J.M., and Fraser, S.E., 2003, MRI: Volumetric imaging for vital imaging and atlas construction, Nat. Cell Biol. Ss10–Ss16.
Jiang, Y., Pandya, K., Smithies, O., and Hsu, E.W., 2004, Three-dimensional diffusion tensor microscopy of fixed mouse hearts, Magn. Reson. Med.52:453–460.
Johnson, G.A., Benveniste, H., Black, R.D., Hedlund, L.W., Maronpot, R.R., and Smith, B.R., 1993, Histology by magnetic resonance microscopy, Magn. Reson. Q 9:1–30.
Johnson, G.A., Cofer, G.P., Fubara, B., Gewalt, S.L., Hedlund, L.W., and Maronpot, R.R., 2002a, Magnetic resonance histology for morphologic phenotyping, J. Magn. Reson. Imaging 16:423–429.
Johnson, G.A., Cofer, G.P., Gewalt, S.L., and Hedlund, L.W., 2002b, Morphologic phenotyping with MR microscopy: The visible mouse, Radiology 222:789–793.
Keng, W.T., Sharpe, J., et al., 2002, Optical projection tomographic examination of miscarried human embryos, J. Med. Genet. 39:S23–S23.
Kerwin, J., Scott, M., Sharpe, J., et al., 2004, 3 dimensional modelling of early human brain development using optical projection tomography, BMC Neurosci. 5:27–27.
Kockenberger, W., 2001, Nuclear magnetic resonance micro-imaging in the investigation of plant cell metabolism, J. Exp. Bot. 52(356):641–652.
Kockenberger, W., De Panfilis, C., Santoro, D., Dahiya, P., and Rawsthorne, S., 2004, High resolution NMR microscopy of plants and fungi, J. Micros. 214(Pt2):182–189.
Kovacevic, N., Henderson, J.T., Chan, E., et al., 2005, Athree-dimensional MRI atlas of the mouse brain with estimates of the average and variability, Cereb. Cortex. 15(5):639–645.
Kuchenbrod, E., Kahler, E., Thurmer, F., Deichmann, R., Zimmermann, U., and Haase, A., 1998, Functional magnetic resonance imaging in intactplants–quantitative observation of flow in plant vessels, Magn. Reson. Imaging 16:331–338.
Lee, S.C., Kim, K., and Kim, J., 2001, One micrometer resolution NMR microscopy, J. Magn. Reson. 150:207–213.
Lo, C., Nabel, E., and Balahan, R., 2003, Meeting report: NHLBI symposium on phenotyping: Mouse cardiovascular function and development, Physiol. Genomics 13(3):185–186.
Louie, A.Y., Huber, M.M., Ahrens, E.T., et al., 2000, In vivo visualization of gene expression using magnetic resonance imaging. Nat. Biotechnol.18(3):321–325.
Mansfield, P., 1977, Multi-planar image formation using NMR spin echoes, J. Phys. C 10:L55–L58.
Manz, B., Volke, F., Goll, D., and Horn, H., 2003, Measuring local flow velocities and biofilm structure in biofilm systems with magnetic resonance imaging (MRI), Biotechnol. Bioeng. 84:424–432.
Masters, B.R., 1999, Early development of optical low-coherence reflectometry and some recent biomedical applications, J. Biomed. Opt. 4:236–247.
Matsuda, Y., Utsuzawa, S., Kurimoto, T., 2003, Super-parallel MR microscope, Magn. Reson. Med. 50:183–189.
Papan, C., Velan, S.S., Fraser, S.E., and Jacobs, R.E., 2001, 3D time-lapse analysis of Xenopus gastrulation movements using mu MRI, Dev. Biol. 235:189.
Paterson-Beedle, M., Nott, K.P., Macaskie, L.E., and Hall, L.D., 2001, Study of biofilm within a packed-bed reactor by three-dimensional magnetic resonance imaging, Methods Enzymol. 337:285–305.
Paulus M.J., Gleason, S.S., Easterly, M.E., and Foltz, C.J., 2001, A review of high resolution X-ray computed tomography and other imaging modalities for small animal research, Lab. Animal 30(3):36–45.
Paulus, M.J., Gleason, S.S., Kennel, S.J., Hunsicker, P.R., and Johnson, D.K., 2000, High-resolution x-ray computed tomography: An emerging tool for small animal cancer research, Neoplasia 2:62–70.
Pautler, R.G., and Koretsky, A.P., 2002, Tracing odor-induced activation in the olfactory bulbs of mice using manganese-enhanced magnetic resonance imaging, Neuroimage 16:441–448.
Pautler, R.G., Mongeau, R., and Jacobs, R.E., 2003, In vivo trans-synaptic tract tracing from the murine striatum and amygdala utilizing manganese enhanced MRI (MEMRI), Magn. Reson. Med. 50:33–39.
Pickhardt, P.J., Halberg, R.B., Taylor, A.J., Durkee, B.Y., Fine, J., Lee, Jr., F.T., and Weichert, J.P., 2005, Microcomputed tomography colonography for polyp detection in an in vivo mouse tumor model. PNAS 102:3419–3422.
Pierpaoli, C., Jezzard, P., Basser, P.J., Barnett, A., and DiChiro, G., 1996, Diffusion tensor MR imaging of the human brain, Radiology 201:637–648.
Robson, S.C., Woods, H.M., et al., 2004, 3-dimensional modelling of human development using optical projection tomography, J. Soc. Gynecol. Invest. 11:296A.
Rollins, A.M., and Izatt, J.A., 1999, Optimal interferometer designs for optical coherence tomography, Opt. Lett. 24:1484–1486.
Rollins, A.M., Kulkarni, M.D., Yazdanfar, S., Ung-arunyawee, R., and Izatt, J.A., 1998, In vivo video rate optical coherence tomography, Opt. Express 3:219–229.
Segars, W.P., Tsui, B.M., Frey, E.C., Johnson, G.A., and Berr, S.S., 2004, Development of a 4-D digital mouse phantom for molecular imaging research, Mol. Imaging Biol. 6:149–159.
Seymour, J.D., Codd, S.L., Gjersing, E.L., and Stewart, P.S., 2004, Magnetic resonance microscopy of biofilm structure and impact on transport in a capillary bioreactor, J. Magn. Reson. 167:322–327.
Shapiro, E.M., Skrtic, S., Sharer, K., Hill, J.M., Dunbar, C.E., and Koretsky, A.P., 2004, MRI detection of single particles for cellular imaging, Proc.Natl. Acad. Sci. USA 101:10901–10906.
Sharpe, J., 2003, Optical projection tomography as a new tool for studying embryo anatomy, J. Anat. 202:175–181.
Sharpe, J., 2004, Optical projection tomography, Annu. Rev. Biomed. Eng. 6:209–228.
Sharpe, J., Ahlgren, U., Perry, P., et al., 2002, Optical projection tomography as a tool for 3D microscopy and gene expression studies, Science 296:541–545.
Song, S.K., Sun, S.W., Ramsbottom, M.J., Chang, C. Russell, J., and Cross, A.H., 2002, Dysmyelination revealed through MRI as increased radial (but unchanged axial) diffusion of water, Neuroimage 17:1429–1436.
Tearney, G.J., Bouma, B.E., Boppart, S.A., Golubovic, B., Swanson, E.A., and Fujimoto, J.G., 1996, Rapid acquisition of in vivo biological images by use of optical coherence tomography, Opt. Lett. 21:1408–1410.
Tearney, G.J., Brezinski, M.E., Bouma, B.E., Boppart, S.A., Pitris, C., Southern, J.F., and Fujimoto, J.G., 1997, In vivo endoscopic optical biopsy with optical coherence tomography, Science 276:2037–2039.
Tuch, D.S., Reese, T.G., Wiegell, M.R., and Wedeen, V.J., 2003, Diffusion MRI of complex neural architecture, Neuron 40:885–895.
Weichert, J.P., 2004, Micro-computed tomography of mouse cancer models, In: Mouse Models of Human Cancer (E.C. Holland, ed.), John Wiley and Sons, New York, pp. 339–348.
Weinmann, H.J., Brasch, R.C., Press, W.R., and Wesbey, G.E., 1984, Characteristics of gadolinium-DTPA complex: A potential NMR contrast agent, AJR Am J Roentgenol 142:619–624.
Weinmann, H.J., Ebert, W., Misselwitz, B., and Schmitt-Willich H., 2003, Tissue-specific MR contrast agents, Eur. J. Radiol. 46:33–44.
Weninger, W., and Mohun, T., 2002, Cardiac phenotyping of transgenic embryos: A rapid 3D-screening method based on episcopic fluorescence imaging capturing (EFIC), Clin. Exp. Pharmacol. Physiol. 29:A70–A71.
Wojtkowski, M., Srinivasan, V.J., Ko, T.H., Fujimoto, J.G., Kowalczyk, A., and Duker, J.S., 2004, Ultrahigh-resolution, high-speed, Fourier domain optical coherence tomography and methods for dispersion compensation, Optics. Express 12(11):2404–2422.
Yazdanfar, S., Kulkarni, M.D., and Izatt, J.A., High resolution imaging of in vivo cardiac dynamics using color Doppler optical coherence tomography, Opt. Express 1:424–431.
Zhang, J., Richards, L.J., Yarowsky, P., Huang, H., van Zijl, P.C., and Mori, S., 2003, Three-dimensional anatomical characterization of the developing mouse brain by diffusion tensor microimaging, Neuroimage 20: 1639–1648.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Tyszka, J.M., Ruffins, S.W., Weichert, J.P., Paulus, M.J., Fraser, S.E. (2006). Related Methods for Three-Dimensional Imaging. In: Pawley, J. (eds) Handbook Of Biological Confocal Microscopy. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-45524-2_34
Download citation
DOI: https://doi.org/10.1007/978-0-387-45524-2_34
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-25921-5
Online ISBN: 978-0-387-45524-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)