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: October 8–9, 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: Workshop Registration Form
- 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 (10/8/26):
Fundamentals of Image Processing in FIJI |
Day 2 (10/9/26):
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
- Generating quantitative measurements from segmented objects
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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].
