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What you will cover in the course
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What you will cover in the course

The main topics of the course 'Introduction to image analysis for plant phenotyping'

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
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Introduction to Image Analysis for Plant Phenotyping

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