What you will cover in the course

The main topics we will cover during this six-week course are as follows:

Week 1 – an introduction to image analysis:

• What is image analysis and how is it used in plant phenotyping?
• What are digital images?
• What to consider when producing digital images

Week 2 – software tools for image analysis:

• Working with images in Fiji (ImageJ)
• Image thresholding
• An introduction to using Python

Week 3 – coding for image analysis:

• An introduction to programming with Python
• The building blocks of programming
• Morphological operations – erosion and dilation

Week 4 – common tasks in image analysis:

• Noise reduction and filtering
• Counting and labelling
• Model-based and feature-based image segmentation

Week 5 – Beyond 2D image data:

• Motion and motion detection in image analysis (video or time sequenced data)
• Volumetric data (3D data stacks)
• Hyperspectral image data

Week 6 – 3D image reconstruction and course summary:

• Why 3D? Example applications
• 3D data types
• An overview of 3D reconstruction approaches
• Discussion and conclusions