May Term Course: Quantitative Fluorescence Microscopy

GCD 8111*/GCD 5111

Dates: May 18 – June 5 (Tu/W/Th/Fr)

Time: 9 a.m. – 1 p.m. (3 credits: A-F) 2-138 MCB (3 week intensive lab course)

Instructor: Sivaraj (Shiv) Sivaramakrishnan (

Course Notes: Graduate students – email instructor about summer/fall enrollment. This course does not conflict with GCD 8171 Literature Analysis 

Course Details

All you ever wanted to know about microscopy and data analysis but were too afraid to ask. You will take microscopes apart (literally) and learn about all the components and settings on common fluorescence microscopes. You will learn the basics of fluorescence and how to select fluorescent proteins and dyes for multi-color imaging. You will learn to use FIJI to analyze number, size, shape, and colocalization using published image data. You will walk away microscopy literate and ready to take control of your primary research data!

Why take it?

  • Learn to use microscopes and quantitatively analyze data. You will have access to fully functional epi-fluorescence microscopes during the entire course.
  • All lab assignments, data analysis, and exam presentations will be completed during the 4 hr morning session (no additional work!).
  • Complete a 3 credit elective class (A-F) in 3 weeks, while learning foundational skills and information that be useful throughout your scientific career.

What do students have to say?

  • “I especially liked explanations of fundamentals that we should remember when thinking about how microscopy and photography work – knowing these will save me a lot of future headaches.”
  • “Stimulated independent learning and [the instructor] worked through problems instead of just talking at us.”
  • “I really appreciated that [we] explored data + images relevant to our current research.”
  • “Instructor was always very responsive to questions in class, which I really appreciated.”

Plankton in Lake Itasca imaged by 2018 MCSB graduate students

Plankton in Lake Itasca imaged by 2018 MCSB graduate students

February, 2020