Tutorial video to use the 'sm-dtw' assessment tool with simulated synthetic phyllotaxis data

This tutorial explain how to use 'sm-dtw', an assessment tool which has been designed to evaluate how good a phyllotaxis measure is from a plant phenotyping experiment. To get data to play with and explore all possible case scenarios, we also designed a program to generate phyllotaxis data and simulate typical errors produced by a phenotyping experiment.

This tutorial explains:

1) the context in which such a tool is useful (what is a phyllotaxis measure ? What kind of phenotyping experiment ? Why do need to evaluate your results ? What are typical errors you want to detect ?)

2) how to download and use the two programs ('sm-dtw' and the generator of phyllotaxis data)

3) how to play with the programs thanks to pedagogical demonstrator notebooks.

In brief, there are 3 notebooks that are meant to be run as three successive steps:

• step1 / Notebook 1: it allows anybody to simulate phyllotaxis data (pair of sequences consisting of ground truth sequences and their error-prone measures),
• step2 / Notebook 2: assess the measure performance with our new program ‘sm-dtw’ (detect errors and quantify precision)
• step3/Notebook 3: control that sm-dtw program correctly interprets the differences between the measure and its ground truth reference.