BASIC BIOINFORMATICS COURSE

The training general objective is to provide basic skills necessary to perform Digital Phenotyping. Specifically, the aim is to train the participants to use tools and approaches using image data to do phenotyping analysis.

Week 1: ImageBreed

• Introduction Basics of Digital Phenotyping

• Drone Phenotyping

• Introduction to ImageBreed

  • Objective: To introduce ImageBreed, a web application for drone data management and analysis

Week 2:  Generic Plant Phenotyping using Ilastik

• Introduction to Machine Learning

• Introduction to Ilastik

  • Objective: To introduce Ilastik as a tool for digital phenotyping and demonstrate its application in biomass estimation for plants

Week 3: Plant disease evaluation using RGB images and ML

• Introduction to Plant Disease Evaluation

• Ilastik Workflow

  • Objective: To demonstrate the application of Ilastik in plant disease evaluation

Week 4: Data Post-Processing

• Basic R and RStudio training

• QC, Checking for Distribution for Normality

•  Adjustments/Transformations

• Other data Exploration/Analysis Method

Week 5: Work on the Project

• Individual Work on the project

• One-on-one meetings with mentors

• Weekly progress report and Group Discussion

Week 6: Work on the Project

• Final Project Report