Basic image processing using Fiji
Basic image processing using Fiji
6 March 2025, 9h30-17h
General context
Recent years, imaging and image processing has become essential for life scientists dealing with scientific images. In Life science, microscopy and imaging have become more and more important. Imaging has evolved from showing examples images towards quantitative biology. Image processing is playing a crucial role and is becoming a means of quantification in life science.
This course aims to introduce and teach the basic concepts of image processing and analysis through hands-on experience using the Fiji distribution of ImageJ. ImageJ is a Java-based image processing and analysis program available in the public domain. It was developed with an open plugin architecture and a built-in development environment, which enables extensive customization and makes it a popular platform for teaching image processing.
The course is divided into two parts. In the first part, participants will learn to perform simple operations on images through a series of short exercises. Advanced features and plugins will also be demonstrated. In the afternoon session, participants will be shown how to use the ImageJ macro language to build an example image analysis pipeline.
This course is designed for researchers working with microscopy images who have little to no experience in image processing. Experienced ImageJ 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.
Trainers
Benjamin Pavie
Amanda Gonçalves
Amanda is a Microscopy Expert at the VIB Bioimaging Core-Gent, where since 2011, she has gained expertise in large sample imaging and quantification, from slide scanner to light sheet. She also has over 15 years of experience teaching science, both practical and theoretical, on the graduate and post graduate levels.
Jérémy Verbeke
Program
Morning session: Image basics and basic operations
Image properties, pixel operations, filters, segmentation, ROI's, registration, pixel classification, and more.
Introduction to ImageJ1 macro language
Practical info
06 March 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
06 March 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
06 March 2025
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.
06 March 2025
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.
06 March 2025
Ghent - VIB/UGent FSVM II
Room: L4 on the fourth floor