Spring 2017

Quantitative Microscopy


Quantitative Fluorescence Microscopy

(GCD 8920 / BIOL 5950)

Spring 2017

Wed & Fri (10-12 pm)

3 credits




An essential primer in quantitative fluorescence microscopy for graduate students and senior undergraduate students in the life sciences

Course Instructor: Sivaraj (Shiv) Sivaramakrishnan (sivaraj@umn.edu)



Fluorescence microscopy is an indispensable technique in the Biological Sciences that is used for studying proteins and cells in their physiological state. While fluorescence microscopy is commonly employed for observing molecules or disease progression, its real strength lies in the ability to reveal quantitative information. The main goal of this course is to introduce the fundamental principles of fluorescence, fluorescence microscopy, and fluorescence quantification to extract maximal information from fluorescence experiments. The course will use ImageJ tutorials along with lectures to provide hands-on expertise in image analysis and interpretation.


Why you should take it? 

Students will gain both a broad understanding of fluorescence microscopy techniques. Graduate students will gain confidence in quantitative analysis of their own image data that is increasingly essential for high-profile publications. Undergraduate students who plan to attend graduate school, medical school, or pursue employment in the biotech industry will find that quantitative microscopy skills will provide them an essential competitive edge


What you will learn? 

In their research, students routinely have to make decisions about experiments involving fluorescence.

  • What is the best fluorescent protein/filter/microscope for a particular experiment?
  • What is an image and how best to display it?
  • What are the measurable quantities in an image, and how to measure them?

Upon completion of this course, students will be enabled to make informed decisions with regards to microscopy technique selection, data acquisition, and data processing.



The course is being offered as satisfactory/no credit (S/N). Class participation and homework assignments based on class participation will account for most of the grade. BIOL 5950 will have a final exam, whereas GCD 8920 will have a mid term exam and a final class presentation.