This is the handbook on optical microscopy. It is often called just `Born and Wolf'. You can find the definition of `optical coordinates', the 3D intensity distribution in the focus of a lens and many other basic concepts here.
Waves in focal regions (Jacob Stamnes)
In this book you find all you want to know about the behavior of light in the focus of a microscope lens.
Electronic light microscopy (David Shotton)
With the subtitle "Techniques in Modern Biomedical Microscopy", this book covers a broad range of topics starting from sampling theory, vital staining & time lapse microscopy to visualization of confocal images.
Introduction to Fourier Optics (Joseph Goodman)
Sometimes referred to as 'Fourier Optics'. A very comprehensive book treating Fourier theory in optics. It provides a thorough theoretical framework.
This is the much improved version of the earlier Gonzalez & Wintz book. You find the digital image processing basics here as well as chapters on image enhancement (filtering) image segmentation and image restoration. A good book to own.
Fourier Transforms and how Fast Fourier transforms work. In addition, there are a few sections on image restoration. Also available is an edition online!!! (http://www.nrbook.com)
(first and second edition) These books cover a broad range of topics in the field of confocal microscopy. You should have them on the shelf, especially the second edition.
Confocal microscopy (Tony Wilson)
This book concentrates more on the theoretical aspects of the confocal microscope. In addition you can find chapters on the design of confocal microscopes here.
Confocal scanning light microscopy with high aperture immersion lenses (Fred Brakenhoff et al)
This early paper is the basic reference for confocal microscopy as we know it today.
Optical fluorescence microscopy in 3 dimensions: microtomoscopy (Roel Wijnaends van Resandt et al) Basic reference for 3D confocal principle of fluorescent objects.
Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index. (Stefan Hell et al).
A thorough study of refractive index mismatch problems.
3D image formation in a high-aperture fluorescence confocal microscope: a numerical analysis (Hans van der Voort and Fred Brakenhoff) Basic reference for high aperture confocal PSF computation. The software used for this paper is a remote ancestor for the PSF generator in the Huygens System.
Various papers of Colin Sheppard.
Sheppard and Wilson have laid the theoretical framework for confocal microscopy. In particular we like Sheppard's papers on the band limits of confocal system (spatial frequency cut-off). Use these if you need a reference for the band limit.
Born, M. & E. Wolf. (1975) Principles of Optics. 5th edn. Pergamon Press, Oxford. Ch 1.
Brakenhoff, G.J., J.S. Binnerts and P. Barends. (1979) Confocal scanning light microscopy with high aperture immersion lenses. J.Micr., Vol 132, pp. 1-7.
Carrington, W., and K. Fogarty (1987) 3-D Molecular distribution in living cells by deconvolution of optical sections using light microscopy. Proceedings of the 13th Annual Northeast Bioengineering Conference. K. Foster ed. IEEE New York, pp. 108-111
Csiszár I. (1991) Why least squares and maximum entropy? An axiomatic approach to inference for linear inverse problems. Ann. Stat., 19, No. 4, pp. 2033-2066.
de Grauw, C.J., J.M. Vroom, H.T.M. van der Voort and H.C. Gerritsen. (1999) Imaging properties in two-photon excitation microscopy and effects of refractive-index mismatch in thick specimens. Appl. Optics, V 38, No. 28, pp 5995-6003.
Dean, P., L. Mascio D. Ow, D. Sudar, J. Mullikin, Proposed standard for image cytometry data files, Cytometry, 1990, 11, pp. 561-569.
Gonzalez, R.C. and R.E. Woods. (1992) Digital Image Processing. Addison-Wesley. ISBN 0-201-50803-6.
Hell, S., G. Reiner, C. Cremer, E.H.K. Stelzer. (1993) Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index. J. Micr., Vol 169, pp. 391-405.
Hell, S.W., M. Schrader, H.T.M. van der Voort. (1997) Far-field fluorescence microscopy with three-dimensional resolution in the 100-nm range. J. Micr., Vol 187, Pt 1, pp. 1-7
Holmes, T.J. (1992) Blind deconvolution of quantum-limited incoherent imagery: maximum-likelihood approach. J. Opt. Soc. Am. A 9 No 7 pp. 1052-1061
Jaynes, E.T. (1982) On the rationale of maximum entropy methods. Proc. IEEE, 70, No. 9, pp.939-951.
Kano, Hiroshi, Hans T.M. van der Voort, Martin Schrader, Geert M.P. van Kempen and Stefan W. Hell. (1996) Avalanche photodiode detection with object scanning and image restoration provided 2-4 fold resolution increase in two-photon fluorescence microscopy. BioImaging 4 '96 p187-197.
Lagendijk, R.L (1990) Iterative Identification and Restoration of Images. Ph. D. Thesis Delft University of Technology, Faculty of Electrical Engineering, information theory group.
Manders, E.M.M. (1994) Dynamics of DNA replication in mammalian cells. Ph. D. Thesis, University of Amsterdam.
Ousterhout, John K., Tcl and the Tk toolkit. 1994. Addison-Wesley, New York. ISBN 0-201-63337-Z
Pawley, J.B. Handbook of biological confocal microscopy. 1990. Plenum Press, New York and London. ISBN 0-306-43538-1
Pawley, J.B. Handbook of biological confocal microscopy. 2nd ed. 1995. Plenum Press, New York and London. ISBN 0-306-448262
Press, W.H., B.P. Flannery, S.A. Teukolsky, W.T. Vetterling. (1992) Numerical Recipes in C , The art of Scientific Computing. Cambridge University Press, U.K. 2nd ed. ISBN 0-521-43108-5
Sheppard, C.J.R., A. Choudhury and J. Gannaway. (1977) Electromagnetic field near the focus of wide-angular lens and mirror systems. IEE J. Microwaves, Opt. Acoust. 1, 129-132.
Sheppard, C.J.R. The spatial frequency cut-off in three-dimensional imaging. (1986a). Optik 72 No. 4 131-133.
Sheppard, C.J.R. The spatial frequency cut-off in three-dimensional imaging II. (1986b). Optik 74 No. 3, pp. 128-129.
Schrader, M., S. W. Hell and H.T.M. van der Voort. (1996) Potential of confocal microscopes to resolve in the 50-100nm range. Appl. Phys. Lett. 69 (24), pp. 3644-3646.
Shotton, D. Electronic light microscopy. (1993) Wiley-Liss New York. ISBN 0-471-56077-4.
Snyder, D.L., T.J. Schulz, J.A. O'Sullivan. (1992) Deblurring subject to nonnegativity constraints. IEEE Trans. Sign. Proc., 40, No. 5, pp. 1143-1150.
Stamnes, J.J. Waves in focal regions. (1986) Adam Hilger, Bristol-Boston.
Tikhonov, A.N. and V.Y. Arsenine. (1977) Solutions of ill-posed problems, Winston/Wiley, Washington.
van der Voort, H.T.M. and G.J. Brakenhoff. (1990) 3D image formation in a high-aperture fluorescence confocal microscope: a numerical analysis. J. Micr., Vol 158, pp. 43-54.
van der Voort, H.T.M. and K.C. Strasters. (1995) Restoration of confocal images for quantitative image analysis. J.Micr., Vol 178, pp. 165-181.
van Kempen, G.M.P., H.T.M. van der Voort, J.G.J. Bauman, K.C. Strasters. (1996) Comparing Maximum Likelihood Estimation and Constrained Tikhonov-Miller Restoration. IEEE Engineering in Medicine and Biology Vol 15, No 1,. pp. 76-83
van Kempen, G.M.P., L.J. van Vliet, P.J. Verveer, H.T.M. van der Voort. (1997) A quantitative comparison of image restoration methods for confocal microscopy. J.Micr., Vol 185, Pt 3, pp.354-365
van Kempen, G.M.P. (1999) Image Restoration in Fluorescence Microscopy. Thesis, Delft University Press, Delft, The Netherlands, ISBN 90-407-1792-3 / CIP.
van Vliet, L.J. (1993) Grey-Scale Measurements in Multi Dimensional Digitized images. Thesis, Delft University Press, Delft, The Netherlands.
Verveer, P. J. and T. M. Jovin. (1997) Acceleration of the ICTM image restoration algorithm. J. Micr., Vol. 188, pp. 191-195.
Verveer, P. J. (1998) Computational and Optical Methods for improving Resolution and Signal Quality in Fluorescence Microscopy. Thesis, Delft University, Delft, The Netherlands.
Vroom, J. M. (1998) Two-photon excitation fluorescence lifetime imaging: development and biological applications. Thesis University Utrecht, ISBN 90-393-1716-X.
Wilson, T. Confocal microscopy. (1990) Academic Press. ISBN 0-12-757270-8.
Wijnaends van Resandt, R.W., H.J.B. Marsman, R. Kaplan, J. Davoust, E.K.H. Stelzer, R. Stricker. (1985), Optical fluorescence microscopy in 3 dimensions: microtomoscopy, J. Micr., Vol 138, pp. 29-34.
Welch, Brent B., Practical Programming in Tcl and Tk. Scnd Ed. 1997 Prentice Hall PTR, New Jersey. ISBN 0-13-616839-2.