Basic Image Processing using Fiji
12 October, 10h -15h, lunch included
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.
- This course is only available for VIB participants
- Note that upon no show without valid justification you will be blacklisted for the VIB training program for 1 year. Click here for more information.
Trainers
Bob Asselbergh
Bob is staff scientist at the VIB Center for Molecular Neurology’s Bio-Imaging Expertise Unit, with an interest in quantitative fluorescence assays, automated high throughput microscopy and superresolution expansion microscopy.
Benjamin Pavie
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
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.
Leuven - Campus Gasthuisberg
O&N5, 5th floor room 404-28.05.347