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Check out the Molecular Expressions and Olympus Fluoview extensive microscopy and cytogenetics book lists, plus there's a wealth of free information available via our external web site links.

Microscopy

Techniques in Confocal Microscopy - Reliable Lab Solutions. P. Michael Conn (2010, Academic press)

Basic Confocal Microscopy. Robert Price, Jay Jerome, editors. (Published December 2010, Springer)

Handbook of Biological Confocal Microscopy. J. B. Pawley editor (2006, 3rd edition, Plenum press)

Confocal Microscopy for Biologists - An Intensive Introductory Course. A. R. Hibbs (2004, Springer Science)

Light and Video Microscopy. Randy O. Wayne (2009, Academic Press)

Fundamentals of Light Microscopy and Electronic Imaging. Douglas B. Murphy (2001, Wiley Liss)

Image Analysis: principles & practice. Joyce Loebl (1985) - a classic easy to read 2D image analysis guide, if you can find it

Imaging Techniques in Cell Biology. Guy Cox editor (2007, CRC Press)

The Royal Microscopy Society Handbook Series - a little dated with some titles deleted, but still useful, e.g. Fluorescence Microscopy: B. Herman, Confocal Laser Scanning Microscopy: C. J. R. Sheppard and D. M. Shotton (Bios Scientific publishers). A new series is about to be launched.

Fluorescence Microscopy of Living Cells in Culture. Part A: Fluorescent Analogs, Labeling Cells and Basic Microscopy (1989: Methods in Cell Biology, Volume 9, Academic Press)

Cell - A Laboratory Manual. Volume 2: Light Microscopy and cell Structure (1998: Cold Spring harbour Laboratory Press)
Volume 2: Culture and Biochemical Analysis of Cells
Volume 3: Sub-cellular Localisation of genes and their Products

Cell biological applications of confocal microscopy. Brian Matsumoto (2002: Methods in Cell Biology 70, Elsevier Science)

Immunocytochemistry

Immunocytochemistry: A practical Guide for Biomedical research. Richard W. Burry (2010, Springer)

Immunohistochemistry: Methods Express Series. Simon Renshaw (2007, Scion Publishing)

Introduction to immunocytochemistry. J. M. Polak & S. Van Noorden (2003, 3rd edition, BIOS Scientific Publishers)

General reading and outreach

Inside the body: Fantastic Images from Beneath the Skin. A book of beautiful optical and electron microscope images of the human body 

Unseen Companions: Big Views of Tiny Creatures. A book full of electron microscope images of the countless tiny creatures, plants, fungi and bacteria that live on or inside our bodies

Heaven and Earth: Unseen by the Naked Eye. Photographic views ranging from the smallest particles on the earth's surface to vast galaxies that are light years away

Molecular cytogenetics

New book: Fluorescence in situ Hybridization (FISH) - Protocols and applications. Joanna M. Bridger, Emanuela V. Volpi, editors (2010, 451 pages, Humana Press)

Fluorescence In Situ Hybridization (FISH) - Application Guide. Thomas Liehr editor (2010, 452 pages, Springer)
Introdution to Fluorescence in situ hybridization, principles and applications. M. Andreeff and D. Pinkel, editors (1999, John Wiley)

Human Cytogenetics. Volume I and II 2nd Edition. D. E. Rooney and B. H. Czepulkowski (1994, IRL Press)

Human Chromosomes. 2nd Edition. R. S. Verma and A. Babu (2002, MacGraw-Hill)

Molecular Cytogenetics - Protocols and Applications. Yao-Shan Fan (2002, Humana Press)

Chromosome Structural Analysis - A Practical Approach. W. A. Bickmore (Oxford University Press)

Human Chromosomes. 4th Edition. O. J. Miller and E. Therman (Springer)