ImageJ Workshop – January 9, 2024

Form Banner

The Advanced Light Microscopy Facility will hold a workshop on digital image analysis using the free program ImageJ.  During the workshop, Facility Director Dr. Chris O’Connell and Facility Scientist Dr. Emery Ng will cover topics ranging from the most basic ImageJ functions through more advanced analysis workflows.  Emphasis will be placed on working with light microscopy images of biological samples.  We will demonstrate common analysis tools with real microscopy data sets and participants will be able to practice on example images.

We will be using the Fiji version of ImageJ.  Fiji is the core ImageJ software that comes bundled with many additional plugins.  Each participant will need to bring their own laptop with Fiji and the sample images installed.  You can download Fiji here into a file location on your computer.  Please verify it is installed and running before the workshop.  Materials and demo images will be provided to registrants beforehand. Contact Chris O’Connell with questions at

Date and Time – Tuesday, January 9th from 9:30-4:30 pm. Lunch will be provided.

Location – Gant, GW003

Enrollment – The workshop is open to all University of Connecticut students, postdocs, and faculty. Attendees must register in advance and space is limited.  There is a $100 registration fee payable by KFS#.

Registration LinkRegistration is now closed.  If you would like to be put on a waiting list in case a spot opens, contact Chris at

Schedule – The following is a tentative schedule of the workshop:

9:30-10:00: Introduction to ImageJ

10:00-10:45: Basic ImageJ functions and manual measurement tools

10:45-12:00: Image thresholding

12:00-1:00: Lunch Break

1:00-2:00: Image thresholding part II and image math

2:00:-2:30 Automated object counting and measurement

2:30-3:00 Coffee Break

3:00-4:00: Colocalization, 3D analysis, measuring objects within objects, and Record/Macro function

4:00-4:30: Helpful tips and image processing ethics