The tutorials are written as jupyter notebooks - browser based Python kernels to run, document, and visualize code (https://jupyter.org/). If you installed Python using Anaconda, it is possible that jupyter is already installed (check with jupyter --version - you should see something like notebook : 6.4.11 in the list that appears). If no list appears, your need to install jupyter notebook first.


  1. Install phenopype` (see installation instructions) and jupyter notebook (pip install jupyter notebook).

  2. Download and unpack the github archive containing the data and code.

  3. Open a terminal in the unpacked folder - don’t forget to activate your conda environment (see warning below).

  4. Start the notebooks with jupyter notebook and click on one of the tutorial files (your browser might give you a security warning - you can ignore it).

  5. Run the code cell by cell inside the browser window (Shift + Enter to run cell and advance).


Make sure you install jupyter notebook to your specific environment (i.e. activate it first using conda activate pp. If not installed in a specific environment, running jupyter notebook will fall back on the conda base environment where phenopype may not be installed (this is a common source of confusion).

Tutorials (read-only)#

Below are the read-only html versions of the code contained in the notebooks - to run them yourself, follow the above instructions. If you want to use the notebooks as a blueprint for your own project, you can also save them as a Python script from a running jupyter notebook using File > Download as > Python (.py).

Tutorial 1

A (very) brief python introduction

  • Python modules

  • Paths and directories

  • Images in Python

Tutorial 2

Interacting with images in phenopype

  • Window control

  • Opening images

  • Creating masks

Tutorial 3

Image analysis workflow

  • Overview

  • Low throughput

  • High throughput

Tutorial 4

The Pype class

  • Operation

  • Configuratiob templates

  • YAML-syntax

Tutorial 5

Setting up and managing projects

  • Project directories

  • Adding images and configs

  • Collecting results

Tutorial 6

Creating and detecting a reference

  • Setting project wide size references

  • Detecting size references

Tutorial 7

Video analysis

  • Motion tracker class

  • Tracking methods