Phenopype: a phenotyping pipeline for Python


Phenopype is a high throughput phenotyping pipeline for Python to support biologists in extracting high dimensional phenotypic data from digital images. The program provides intuitive, high level computer vision functions for image preprocessing, segmentation, and feature extraction. Users can assemble their own function-stacks that can be stored in the human-readable `yaml`-format along with raw data and results, facilitating high throughput and full data reproducibility. Phenopype can be run from Python or from a Python Integrated Development Environment (IDE), like Spyder. Phenopype is designed to provide robust image analysis workflows that can be implemented with little or no Python experience.

Getting started:
  1. Install Phenopype - via the Python Package Index (PYPI): pip install phenopype
  2. Run the Tutorials - Tutorial 1 is for Python beginners, otherwise Tutorial 2 is a good starting point
  3. Check the Examples - Example 1 delineates a typical computer vision workflow