Biology 3333/5433 - Advanced Microscopy Techniques

Dr. Sheffield

Tuesday and Thursday, 12:30-1:50, BLS 332 - and scheduled labs in BLS 348

Textbook: Murphy, Douglas and Davidson, Michael, Fundamentals of Light Microscopy and Electronic Imaging, 2nd Edition.  Wiley-Blackwell, 2013.  Note, the Second Edition is required, not the first.

The purpose of this course is to investigate the variety of image transforms that are possible using the light and electron microscope. The first half of the course, approximately, will cover basic principles of optics - the nature of light, diffraction, refraction, etc., the nature of lenses, and the design of the light microscope. We will discuss phase contrast, dark field, interference contrast, and modulation contrast, as well as polarization and fluorescence microscopy. We will also discuss the use of different labeling procedures to obtain more information about samples. We will then consider several scanning microscope systems, including the scanning confocal microscope and the scanning electron microscope. These systems will be demonstrated in laboratory experiences.

The second half will be devoted to digital transformation of images. We will discuss the nature of digital images, the concepts of LUTs and transforming filters, as well as image mathematics. We will also consider the application of conventional image processing programs to microscopic samples.

Each student will be also expected to select a microscopy project. Time will be divided between laboratory experiences with the different microscopes, and class discussion of the projects in process. Examples of projects by students in the past can be found here :

Much of the resource material will be on the flash drive that is distributed in class, although I will expect you to use additional resources when appropriate.

Grading will be based on two exams, scheduled after the first and second halves of the semester, and the results of the project. The results of the project will be presented orally at the regularly scheduled Final Exam time (Tuesday 5/9 from 1-3 pm.  You will be expected to return the flash drive, with your collected images, and the final presentation, at the end of the class.

The class schedule is here:

The fine print:

First class: Tuesday, Jan. 22

Last day to drop (tuition refund available): Monday, February 4

Spring recess: No classes are held during the week March 10 - March 16.

Last day to withdraw (no refund): Monday, March 26.

Last Class: Thursday, May 2.