Selected Literature References

Books

• Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light, 7th edition., Born, M. and Wolf, E., Cambridge University Press, Cambridge, United Kingdom, 952 pages (1999).
• Video Microscopy (Methods in Cell Biology, 56)., Sluder, G. and Wolf, D. (eds), Academic Press, New York, 334 pages (1998).
• Deconvolution of Images and Spectra, 2nd edition., Jansson, P. (ed), Academic Press, San Diego, California, 514 pages (1997).
• Introduction to Fourier Optics., Goodman, J., McGraw-Hill, New York, 441 pages (1996).
• Digital Image Processing: Principles and Applications., Baxes, G., John Wiley and Sons, New York, 452 pages (1994).
• Digital Image Processing., Castleman, K., Prentice-Hall, Englewood Cliffs, New Jersey, 667 pages (1979).

Review Articles

• Image-restoration methods: basics and algorithms., Boccacci, P. and Bertero, M., in Confocal and Two-Photon Microscopy: Foundations, Applications, and Advances, Diaspro, A. (ed), Wiley-Liss, New York, pages 253-269 (2002).
• A workingperson's guide to deconvolution in light microscopy., Wallace, W., Schaefer, L., and Swedlow, J., in BioTechniques, 31(5), pages 1076-1097 (2001).
• Contrast, resolution, bleaching and statistics in confocal microscopy., Pawley, J., in Focus on Multidimensional Microscopy, Cheng, P., Hwang, P., Wu, J., Wang, G., and Kim, H. (eds), World Scientific, Singapore, pages 134-141 (1999).
• Three-dimensional imaging by deconvolution microscopy., McNally, J., Karpova, T., Cooper, J., and Conchello, J., in Methods, 19, pages 373-385 (1999).
• Computational deblurring of fluorescence microscope images., Shaw, P., in Cell Biology: A Handbook, 2nd edition, Academic Press, San Diego, California, pages 206-217 (1998).
• Confocal microscopy and deconvolution techniques., Spector, D., Goldman, R., and Leinwand, L., in Cells: A Laboratory Manual, Volume 2, Light Microscopy and Cell Structure, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pages 96.1-96.23 (1998).
• High resolution 3-D imaging of living cells by image restoration., Carrington, W., Fogarty, K., Lifshitz, L., and Tuft, R., in Imaging Living Cells, Rizzuto, R. and Fasolato, C. (eds), Springer-Verlag, Heidelberg, Germany, pages 30-50 (1998).
• Alternating projections onto convex sets., Marks, R., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 478-501 (1997).
• Application to electron spectroscopy for chemical analysis., Davies, R. and Jansson, P., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 265-283 (1997).
• Convergence of relaxation algorithms., Crilly, P., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 183-199 (1997).
• Convolution and related concepts., Jansson, P., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 1-41 (1997).
• Deconvolution., Inoué, S. and Spring, K., in Video Microscopy: The Fundamentals, 2nd edition, Plenum Press, New York, pages 549-552 (1997).
• Deconvolution examples., Crilly, P., Blass, W., and Halsey, G., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 236-263 (1997).
• Deconvolution in optical microscopy., Swedlow, J., Sedat, J. and Agard, D., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 284-309 (1997).
• Deconvolution of Hubble Space Telescope images and spectra., Hanisch, R., White, R., and Gilliland, R., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 310-360 (1997).
• Distortion of optical spectra., Jansson, P., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 42-75 (1997).
• Fourier spectrum continuation., Howard, S., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 398-426 (1997).
• Instrumental considerations., Blass, W. and Halsey, G., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 203-235 (1997).
• Maximum probable estimates of spectra., Frieden, B., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 361-396 (1997).
• Minimum-negativity-constrained Fourier spectrum continuation., Howard, S., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 428-475 (1997).
• Modern constrained nonlinear methods., Jansson, P., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 107-181 (1997).
• Traditional linear deconvolution methods., Jansson, P., in Deconvolution of Images and Spectra, 2nd edition, Jansson, P. (ed), Academic Press, San Diego, California, pages 76-106 (1997).
• Image restoration and three-dimensional image processing., Castleman, K., in Digital Image Processing, Prentice-Hall, Upper Saddle River, New Jersey, pages 387-430; 563-602 (1996).
• Comparison of wide-field/deconvolution and confocal microscopy for 3D imaging., Shaw, P., in Handbook of Biological Confocal Microscopy, 2nd edition, Pawley, J. (ed), Plenum Press, New York, pages 373-388 (1995).
• Light microscopic images reconstructed by maximum likelihood deconvolution., Holmes, T., Bhattacharyya, S., Cooper, J., Hanzel, D., Krishnamurthi, V., Lin, W.-C., Roysam, B., Szarowski, D., and Turner, J., in Handbook of Biological Confocal Microscopy, 2nd edition, Pawley, J. (ed), Plenum Press, New York, pages 389-402 (1995).
• Scattering by Particles., Bohren, C., in Handbook of Optics, volume 1, Bass, M. (ed), McGraw-Hill, New York, pages 6.1-6.18 (1995).
• Signal-to-noise in confocal microscopes., Sheppard, C., Gan, X., Gu, M., and Roy, M., in Handbook of Biological Confocal Microscopy, 2nd edition, Pawley, J. (ed), Plenum Press, New York, pages 363-372 (1995).
• The collection, processing, and display of digital three-dimensional images of biological specimens., Chen, H., Swedlow, J., Grote, M., Sedat, J. and Agard, D., in Handbook of Biological Confocal Microscopy, 2nd edition, Pawley, J. (ed), Plenum Press, New York, pages 197-210 (1995).
• Background rejection and optimization of signal to noise in confocal microscopy., Sandison, D., Piston, D., and Webb, W., in Three-Dimensional Confocal Microscopy: Volume Investigation of Biological Specimens, Stevens, J., Mills, L. and Trogadis, J. (eds), Academic Press, San Diego, California, pages 29-46 (1994).
• Sources of noise in three-dimensional microscopical data sets., Pawley, J., in Three-Dimensional Confocal Microscopy: Volume Investigation of Biological Specimens, Stevens, J., Mills, L. and Trogadis, J. (eds), Academic Press, San Diego, California, pages 47-94 (1994).
• Computer reconstruction in three-dimensional fluorescence microscopy., Shaw, P., in Electronic Light Microscopy: The Principles and Practice of Video-Enhanced Contrast, Digital Intensified Fluorescence, and Confocal Scanning Light Microscopy, Shotton, D. (ed), John Wiley & Sons, London, United Kingdom, pages 211-230 (1993).
• Design and construction of an optimal illumination system for quantitative wide-field multi-dimensional microscopy., Kam, Z., Jones, M., Chen, H., Agard, D., and Sedatin, J., in Bioimaging, 1, pages 71-81 (1993).
• Rapid scanning confocal microscopy., Art, J. and Goodman, M., in Cell Biological Applications of Confocal Microscopy (Methods in Cell Biology, 38), Matsumoto, B. (ed), Academic Press, San Diego, California, pages 62-64 (1993).
• Three-dimensional fluorescence microscopy., Shaw, P. and Rawlins, D., in check (Progress in Biophysics and Molecular Biology, 56), check (ed), check, check, check, pages 187-213 (1991).
• Video and opto-digital imaging microscopy - computational deblurring of fluorescent images., Shotton, D., in New Techniques of Optical Microscopy and Microspectroscopy (Topics in Molecular and Structural Biology), Cherry, R. (ed), CRC Press, Boca Raton, Florida, pages 28-40 (1991).
• Fluorescence microscopy in three dimensions., Agard, D., Hiraoka, Y., Shaw, P., and Sedat, J., in Fluorescence Microscopy of Living Cells in Culture (Methods in Cell Biology, 30), Taylor, P. and Wang, Y. (eds), Academic Press, San Diego, California, pages 353-377 (1990).
• Image fidelity: characterizing the imaging transfer function., Young, I., in Fluorescence Microscopy of Living Cells in Culture (Methods in Cell Biology, 30), Taylor, P. and Wang, Y. (eds), Academic Press, San Diego, California, pages 1-45 (1989).
• Optical sectioning microscopy: cellular architecture in three dimensions., Agard, D., in Annual Review of Biophysics and Bioengineering, 13, pages 191-219 (1984).
• Image enhancement and restoration., Frieden, B., in Picture Processing and Digital Filtering (Topics in Applied Physics, 6), Huang, T. (ed), Springer-Verlag, New York, pages 177-248 (1975).

Research Reports

• Computational adaptive optics for live three-dimensional biological imaging., Kam, Z., Hanser, B., Gustafsson, M., Agard, D., and Sedat, J., in Proceedings of the National Academy of Sciences of the United States of America, 98(7), pages 3790-3795 (2001).
• Generalized approach for accelerated maximum likelihood based image restoration applied to three-dimensional fluorescence microscopy., Schaefer, L., Schuster, D., and Herz, H., in Journal of Microscopy, 204(2), pages 99-107 (2001).
• Location of the initiation site of calcium transients and sparks in rabbit heart Purkinje cells., Cordeiro, J., Spitzer, K., Giles, W., Ershler, P., Cannell, M., and Bridge, J., in Journal of Physiology, 531(2), pages 301-14 (2001).
• Blind deconvolution of 3D transmitted light brightfield micrographs., Holmes, T. and O'Connor, N., in Journal of Microscopy, 200(2), pages 114-127 (2000).
• Live cell imaging by multifocal multiphoton microscopy., Straub, M., Lodemann, P. Holroyd, P., Jahn, R., and Hellin, S., in European Journal of Cell Biology, 79(10), pages 726-34 (2000).
• Transient sister chromatid separation and elastic deformation of chromosomes during mitosis in budding yeast., He, X., Asthana, S., and Sorger, P., in Cell, 101(7), pages 763-775 (2000).
• A comparison of image restoration approaches applied to three-dimensional confocal and wide-field fluorescence microscopy., Verveer, P., Gemkow, M., and Jovin, T., in Journal of Microscopy, 193(1), pages 50-61 (1999).
• Equivalence of the Huygens-Fresnel and Debye approach for the calculation of high aperture point-spread functions in the presence of refractive index mismatch., Egner, A. and Hell, S., in Journal of Microscopy, 193(3), pages 244-249 (1999).
• Live cell fluorescence imaging of T cell MEKK2: redistribution and activation in response to antigen stimulation of the T cell receptor., Schaefer, B., Ware, M., Marrack, P., Fanger, G., Kappler, J., Johnson, G., and Monks, C., in Immunity, 11(4), pages 411-421 (1999).
• Assembly and function of the actin cytoskeleton of yeast: relationships between cables and patches., Karpova, T., McNally, J., Moltz, S., and Cooperin, J., in Journal of Cell Biology, 142(6), pages 1501-1517 (1998).
• Superresolution and convergence properties of the expectation-maximization algorithm for maximum-likelihood deconvolution of incoherent images., Conchello, J., in Journal of the Optical Society of America A, 15(10), pages 2609-2619 (1998).
• Visualization of single RNA transcripts in situ., Femino, A., Fay, F., Fogarty, K., and Singer, R., in Science, 280(5363), pages 585-590 (1998).
• Dispersion, aberration and deconvolution in multi-wavelength fluorescence images., Scalettar, B., Swedlow, J., Sedat, J., and Agard, D., in Journal of Microscopy, 182(1), pages 50-60 (1996).
• Perturbation of nuclear architecture by long-distance chromosome interactions., Dernburg, A., Broman, K., Fung, J., Marshall, W., Philips, J., Agard, D., and Sedat, J., in Cell, 85(5), pages 745-759 (1996).
• Blind deconvolution of fluorescence micrographs by maximum-likelihood estimation., Krishnamurthi, V., Liu, Y.-H., Bhattacharyya, S., Turner, J., and Holmes, T., in Applied Optics, 34(29), pages 6633-6647 (1995).
• Comparison of three-dimensional imaging properties between two-photon and single-photon fluorescence microscopy., Gu, M. and Sheppard, C., in Journal of Microscopy, 177(2), pages 128-137 (1995).
• Restoration of confocal images for quantitative image analysis., van der Voort, H. and Strasters, K., in Journal of Microscopy, 178(2), pages 165-181 (1995).
• Superresolution three-dimensional images of fluorescence in cells with minimal light exposure., Carrington, W., Lynch, R., Moore, E., Isenberg, G., and Fay, F., in Science. 268, pages 1483-1487 (1995).
• Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index., Hell, S., Reiner, G., Cremer, C., and Stelzer, E., in Journal of Microscopy, 169(3), pages 391-405 (1993).
• Image sharpness and contrast transfer in coherent confocal microscopy., Oldenbourg, R., Terada, H., Tiberio, R., and Inoué, S., in Journal of Microscopy, 172(1), pages 31-39 (1993).
• Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide field microscopy., Swedlow, J., Sedat, J., and Agard, D., in Cell, 73, pages 97-108 (1993).
• Blind deconvolution of quantum-limited imagery: maximum likelihood approach., Holmes, T., in Journal of the Optical Society of American A, 9(7), pages 1052-1061 (1992).
• Regularized linear method for reconstruction of three-dimensional microscopic objects from optical sections., Preza, C., Miller, M., Thomas L., and McNally, J., in Journal of the Optical Society of America A, 9(2), pages 219-228 (1992).
• Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy., Gibson, S. and Lanni, F., in Journal of the Optical Society of America A, 8(10), pages 1601-1613 (1991).
• Single particle tracking: analysis of diffusion and flow in two-dimensional systems., Qian, H., Sheetz, M., and Elson, E., in Biophysical Journal, 60(4), pages 910-921 (1991).
• The point-spread function of a confocal microscope: its measurement and use in deconvolution of 3-D data., Shaw, P. and Rawlins, D., in Journal of Microscopy, 163(2), pages 151-165 (1991).
• 3-D image formation in high-aperture fluorescence confocal microscopy: a numerical analysis., van der Voort, H. and Brakenhoff, G., in Journal of Microscopy, 158(1), pages 43-54 (1990).
• Determination of three-dimensional imaging properties of a light microscope system: partial confocal behavior in epifluorescence microscopy., Hiraoka, Y., Sedat, J., and Agard, D., in Biophysical Journal, 57, pages 325-333 (1990).
• Image restoration in 3D microscopy with limited data., Carrington, W., in Proceedings of SPIE The International Society for Optical Engineering, 1205, pages 72-83 (1990).
• Three-dimensional organization of ribosomal DNA in interphase nuclei of Pisum sativum by in situ hybridization and optical tomography., Rawlins, D. and Shaw, P., in Chromosoma (Berlin), 99, pages 143-151 (1990).
• Expectation-maximation restoration of band-limited, truncated point-process intensities with application in microscopy., Holmes, T., in Journal of the Optical Society of America A, 6(7), pages 1006-1014 (1989).
• Three-dimensional molecular distribution in single cells analysed using the digital imaging microscope., Fay, F., Carrington, W., and Fogarty, K., in Journal of Microscopy, 153(2), pages 133-149 (1989).
• Tilted view reconstruction in optical microscopy., Shaw, P., Agard, D., Hiraoka, Y., and Sedat, J., in Biophysics Journal, 55, pages 101-110 (1989).
• Three-dimensional organization of chromosomes of Crepis capillaris by optical tomography., Rawlins, D. and Shaw, P., in Journal of Cell Science, 91, pages 401-414 (1988).
• The use of a charge-coupled device for quantitative optical microscopy of biological structures., Hiraoka, Y., Sedat, J., and Agard, D., in Science, 238, pages 36-41 (1987).
• Reconstructing 3-D light-microscopic images by digital image processing., Erhardt, A., Zinser, G., Komitowski, D., and Billie, J., in Applied Optics, 24(2), pages 194-200 (1985).
• Three-dimensional architecture of a polytene nucleus., Agard, D. and Sedat, J., in Nature, 302, pages 676-681 (1983).
• An iterative unfolding method for response matrices., Gold, R., in United States Atomic Energy Commission Report, ANL-6984, Argonne National Laboratory, Argonne, Illinois, (1964).