Workshop on Optical Microscopy

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Optical microscopy provides a quick, direct method to visualize and measure objects on the microscale. Diverse microscopy tools and techniques enable a unique insight into biological processes at the cellular level. To successfully integrate microscopy in your lab routine, understanding the mechanism of optical microscopy is essential.

Course Description

This workshop will provide a practical guide on how to use optical microscopy in the natural and life sciences. It will give participants the necessary tools to design, conduct, and analyze light microscopy experiments, particularly bright-field and fluorescence (confocal) microscopy. It will also enable you to better evaluate microscopy data presented in the scientific literature. Finally, you will learn about the microscopy core facility at Georgia Tech, so you can immediately start to plan and discuss your own experiments.

The workshop is suitable for any (undergrad/grad) student or postdoc at the beginner to intermediate level in optical microscopy. Participants with backgrounds from life/medical sciences, biology, physical sciences, and related areas are welcome.

Learning Outcomes

By the end of the workshop, participants will be able to:

  1. Explain the basic physical concepts of light microscopy
  2. Identify challenges that come with imaging, especially with biological samples
  3. Distinguish between different microscopy designs and their application
  4. Define the appropriate experimental setting to visualize a certain sample/feature
  5. Conduct a basic microscopy measurement using transmission and confocal microscopy
  6. Apply image analysis tools to analyze microscopy images quantitatively


June 26, 2019

11 AM: Welcome, coffee

11:15 AM – 01:15 PM: Introduction to optical microscopy; basics in optics

and microscopy setup

1:15 – 2:15 PM: Lunch break

2:15 – 3:30 PM: Optical resolution, visualization, and contrast (brightfield/fluorescence)

3:45 – 5:00 PM: Advanced microscopy techniques; presentation of Georgia Tech Optical Microscopy Core Facility by Aaron Lifland

June 27, 2019

10:30 – 11:45 AM: Lab tour, group 1 

12:00 – 1:00 PM: Lunch break

1:00 – 2:15 PM: Image analysis using Fiji /ImageJ, part 1

2:30 – 3:45 PM: Image analysis using Fiji /ImageJ, part 2

4:00 – 5:15PM: Lab tour, group 2

Register at https://forms.gle/6R1FFVcrhwUHKDqUA. Space is limited to 40 participants.

About the Instructor

Gabi Steinbach is a postdoctoral fellow in the research group of Peter Yunker, in the School of Physics. She studies spatial structures and emerging dynamics in bacterial communities. She received her Ph.D. in 2016 from Chemnitz University of Technology, Germany, for her work on the self-organization of magnetic colloids using microscopy.

Attendee Preparation

Participants should bring their own laptop. They should have downloaded Fiji, a platform-independent, Java-based application that requires no installation on your system. Participants are encouraged to discussi their current research project during the workshop and think about how microscopy can advance or complement their work.


  • Workflow Status: Published
  • Created By: A. Maureen Rouhi
  • Created: 06/05/2019
  • Modified By: A. Maureen Rouhi
  • Modified: 06/06/2019