Software

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 Python package is in beta stage and currently under code-review by the pyOpenSci community. Visit the package homepage to get started!

Guides

Interactive plotting in R and Python

https://github.com/mluerig/Interactive-plotting-platforms
A virtual presentation I gave at Eawag’s first symposium of reproducible research, organized by Carlos Melian.