Day 1 - 17 November
Day 2 - 18 November
Day 3 - 19 November
9:30 AM
— 11:00 AM
Working with ImageJ
- Fiji and ImageJ
- ImageJ interface
- Basic concepts and common tasks
- Opening, visualizing and saving an image
11:00 AM
— 11:20 AM
Coffee Break
11:20 AM
— 12:30 PM
Exercises
12:30 PM
— 2:00 PM
Lunch
2:00 PM
— 3:00 PM
Multi-dimensional images
- 5D images: x, y, z, channels and time
- Basic operations
3:00 PM
— 3:15 PM
Coffee Break
3:15 PM
— 4:30 PM
Exercises
9:30 AM
— 11:00 AM
Quantitative bioimage analysis
- Images as a source of data
- Regions of interest
- Line profile
- ROI Manager
11:00 AM
— 11:20 AM
Coffee Break
11:20 AM
— 12:30 PM
Exercises
12:30 PM
— 2:00 PM
Lunch
2:00 PM
— 3:00 PM
Spatial measurements in ImageJ
- Pixel spatial calibration
- Setting a scale bar
- Measurement types
3:00 PM
— 3:15 PM
Coffee Break
3:15 PM
— 4:30 PM
Exercises
9:30 AM
— 11:00 AM
Image pre-processing and segmentation
- Basics of linear filtering
- Thresholding
- Basics of Binary filtering
- Object counting
11:00 AM
— 11:20 AM
Coffee Break
11:20 AM
— 12:30 PM
Exercises
12:30 PM
— 2:00 PM
Lunch
2:00 PM
— 3:00 PM
Advanced Segmentation
- Labkit
- Stardist
3:00 PM
— 3:15 PM
Coffee Break
3:15 PM
— 4:15 PM
Introduction to automation
- Using the macro recorder
- Introduction to batch processing
- Best practices in reporting bioimage quantification
4:15 PM
— 5:00 PM
Exercises and Wrap-Up