phenopype: a phenotyping pipline for Python

phenopype is a high throughput phenotyping package for the programming language Python. It aims at supporting biologists in their efforts to extract high dimensional phenotypic data from digital images. phenopype provides high level functions for image processing that can be stacked and executed sequentially to efficiently process single images or large data sets. Users can interactively assemble their own function-stacks that can be customized and stored along with raw data for full reproducibility. Phenopype is designed to provide robust image analysis workflows that can be implemented with little or no Python experience.

The package was code reviewed by the pyOpenSci consortium and published in Methods in Ecology and Evolution. To get started visit

I use phenopype as a starting point in many of my image analysis workflows:


Interactive plotting in R and Python


Computer vision