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Summary and next steps

A summary of week 2 of inroduction to image analysis for plant phenotyping

This week week in the course we have covered:

  • Using Fiji to measure image features such as distance, angle, area, and how to calibrate those measurments
  • Image histograms: what they represent and how they can be used and interpreted
  • Binary image thresholding and some of the automated algorithms for thresholding in Fiji
  • The use of morphological operations such as dilation and erosion to ‘tidy up’ thresholded images
  • The use of the script editor in Fiji for automation and batch processing
  • Colour thresholding and the use of alternative colour space to the RGB model such as the HSB model
  • The basics of running Python code on your computer
  • This includes: using the command line, and installing and using libraries

Next week, we’ll look at Python programming in more detail, and how it can be used in image analysis.

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Introduction to Image Analysis for Plant Phenotyping

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