a phenotyping pipeline for python
Project description
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
- Install Phenopype - via the Python Package Index (PYPI):
pip install phenopype
- Run the Tutorials - Tutorial 1 is for Python beginners, otherwise Tutorial 2 is a good starting point
- Check the Examples - Example 1 delineates a typical computer vision workflow
Documentation
Full documentation can be found here: https://mluerig.github.io/phenopype/
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