Microscopy Class


Enrolment capacity = 12 (10 undergraduate, 2 graduate)

If grad student spaces are not filled they may be opened for undergraduates. Please contact Dr Bannigan if you want to enrol in this class but e-campus shows it as full.

The Instructor :

Dr Alex Bannigan

Room 052 Burruss
Phone: 540-568 4521
Email: bannigax@jmu.edu

Office Hours :

Fall 2011:

  • Mon 2pm-4pm
  • Wed 9am-11am
  • Thu 9am-10:30am

Class times/locations:

  • Tue/Thur 12:30pm-3:35pm
  • Burruss 034 (lecture), 052 (lab)

Students are welcome to come by outside these times, but I cannot guarantee that I will be there or available for consultation. Emails will not be read or answered between 6pm and 8am or on weekends.

Objectives :

On completion of this course, students will be able to:


  • Use any microscope effectively
  • Troubleshoot problems when using a microscope
  • Prepare specimens for microscopy
  • Effectively present results gathered using microscopy


  • Explain properties of light such as wavelength, phase, refraction and polarization
  • Predict the effect that changing settings on the microscope will have on the quality of the image.
  • Identify the focal planes in a microscope’s optic path
  • set up a microscope for Koehler illumination and DIC
  • select appropriate fluorophores and filters for fluorescent labeling
  • Explain the relative advantages of different kinds of microscopy and the circumstances under which they should be used
  • use a confocal microscope
  • Capture digital images that provide the maximum possible information
  • Make quantitative measurements from digital fluorescence micrographs
  • List the fundamental differences between light and electron microscopy
  • Design an experiment using microscopy
  • Critically assess microscopy results presented in journal articles
  • Make a figure for publication


Recommended Texts (available in the JMU library)

N.B. There is no required text for this class

Murphy, Douglas B. (2001) Fundamentals of light microscopy and electronic imaging. Wiley-Liss (Library Call # QH211 .M87 2001)

Herman, B. (1997) Fluorescence Microscopy (2nd edition). Bios Scientific Publishers. (Library Call #: QH212.F55 H47 1998)

Pawley, James B. (2006) Handbook of Biological Confocal Microscopy (3rd edition). Springer. (Library Call #: QH224 .H36 2006 )













Microscopy Facility, Biology Department, James Madison University, Harrisonburg, VA

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