Workshop: Basic Image Processing and 2D Segmentation with FIJI (7/23-7/24, 2026)

Workshop: Basic Image Processing and 2D Segmentation with FIJI

The University Imaging Centers (UIC) invites researchers to participate in Basic Image Processing and 2D Segmentation with FIJI, a hands-on, introductory workshop designed for first-time users of FIJI/ImageJ.

Over two mornings, participants will learn core image-processing and segmentation techniques commonly used in biological and biomedical imaging workflows. This workshop is intended for beginners; individuals with intermediate or advanced FIJI experience are welcome to register but may find the content too introductory.

Workshop Details

Dates: July 23–24, 2026
Time: 9AM - 12PM on both days
Location: UIC Snyder Hall, Room 13
Capacity: Limited to 17 participants. Seats will be reserved on a first-come-first-served basis.
Fee: $120 per person (For participants from rate-supporting units, 25% of the registration cost will be covered.)
Registration: https://forms.gle/1kXo6mNCinoRiqJP9

Participants should bring their own laptop with at least 8 GB of RAM. Workshop materials, including sample images and the FIJI application, will be provided through a shared Google Drive folder.

What You'll Learn

Day 1 (7/23/26): Fundamentals of Image Processing in FIJI	Day 2 (7/24/26): Introduction to 2D Segmentation and Quantification
Installing, updating, and configuring FIJI Managing plugins and memory settings Navigating the FIJI graphical user interface Opening and duplicating images Understanding image metadata and histograms Adjusting brightness, contrast, and look-up tables Restoring spatial calibration and adding scale bars Understanding sources of image noise Basic image enhancement techniques, including: Denoising Line intensity profile analysis Rolling-ball background subtraction Image smoothing and sharpening filters Local contrast enhancement	Understanding different segmentation approaches Detecting regional maxima Cell counting using regional maxima Selecting quantitative measurements Segmenting nuclei using the StarDist2D plugin Generating quantitative measurements from segmented objects

Day 1 (7/23/26):
Fundamentals of Image Processing in FIJI

Day 2 (7/24/26):
Introduction to 2D Segmentation and Quantification

Installing, updating, and configuring FIJI
Managing plugins and memory settings
Navigating the FIJI graphical user interface
Opening and duplicating images
Understanding image metadata and histograms
Adjusting brightness, contrast, and look-up tables
Restoring spatial calibration and adding scale bars
Understanding sources of image noise
Basic image enhancement techniques, including:
- Denoising
- Line intensity profile analysis
- Rolling-ball background subtraction
- Image smoothing and sharpening filters
- Local contrast enhancement

Understanding different segmentation approaches
Detecting regional maxima
Cell counting using regional maxima
Selecting quantitative measurements
Segmenting nuclei using the StarDist2D plugin
Generating quantitative measurements from segmented objects

Workshop Format

Day 1 (3 hrs) will consist of:	Day 2 (2.5 hrs) will consist of:
Two 40-minute instructional lectures Two 45-minute guided hands-on exercise sessions	One 40-minute lecture One 50-minute guided, hands-on exercise session One 60-minute session for additional questions and consultation on individual projects

If you have any questions about this workshop, please reach out to the UIC team at [email protected].