Basic image processing using Fiji
Basic image processing using Fiji
1 October 2026, 9h30- 17h00
General context
As microscopy has become central to life science research, the ability to process and analyze image data is essential for PhD students, postdocs, and technical staff working with biological images. This introductory training offers a hands-on approach to image processing with Fiji, an open-source platform based on ImageJ.
You will learn to perform basic image processing tasks, apply filters, and use plugins for biological image quantification. This includes using built-in machine learning and neural network methods for image segmentation tasks. The course also covers automating repetitive tasks with macros, enabling more efficient and reproducible workflows. By the end of the session, you will have the practical skills to analyze microscopy images and develop simple analysis pipelines for your research.
- Identify core Fiji interface components and describe their functions in image analysis.
- Apply standard image processing operations (e.g., filtering, thresholding, segmentation).
- Use key Fiji plugins for common life science image analysis tasks.
- Evaluate image analysis quality and accuracy by comparing processed and raw data.
- Create simple image analysis workflows and build a Fiji macro for batch processing.
- Modify existing macro scripts to specific experimental needs.
This course uses a strong hands-on approach with guided exercises in Fiji.
This course is designed for researchers working with microscopy images who have little to no experience in image processing. Experienced Fiji users may find limited novelty in the content.
No prior knowledge is required to join this course. Participants are requested to bring their own laptop, Fiji pre-installed.
Fiji
This course is part of the learning path Bioimaging.
AI methods used
The course explores machine learning and neural network methods for image segmentation, covering Random Forest–based pixel classification with Trainable Weka Segmentation and a neural network for nucleus segmentation (StarDist). The course includes demonstrations of cell segmentation (Cellpose) and general-purpose object segmentation (Segment Anything Model - SAM).
Trainers
Program
Morning session: Image basics and basic operations
Introduction to ImageJ1 macro language
Practical info
01 October 2026
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
01 October 2026
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
01 October 2026
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
01 October 2026
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.