phenopype 1.0.3

a phenotyping pipeline for python

Phenopype: a phenotyping pipeline for Python

Phenopype is a high throughput phenotyping pipeline for Python that aims at supporting biologists in their efforts to extract high dimensional phenotypic data from digital images. Phenopype provides high level image-preprocessing, -segmentation, and -analysis functions that can be executed sequentially in a semi or fully automated fashion. Users can assemble their own function-stacks that can be customized and stored along with raw data for full 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

Documentation

Full documentation can be found here: https://mluerig.github.io/phenopype/