phenopype A phenotyping pipeline for Python

Welcome to the phenopype gallery!

Check out the projects below to get a feeling for which sort of image analysis problems can be tackled with phenopype: either run the code yourself (follow the provided instructions) or just check out the read only html version of the notebooks. If you found a bug in the package or any of these materials, please raise an issue in the main phenopype repo on GitHub.


(Analogous to the phenopype tutorials)

  1. Install phenopype (pip install phenopype) 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).

  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).

Additional dependencies: ipyplot to display images in the notebooks: (pip install ipyplot), and trackpy to analyze the data collected in project 4 (pip install trackpy).