phenopype 1.0.9

a phenotyping pipeline for python

Phenopype: a phenotyping pipeline for Python

Author: Moritz Lürig
License: LGPL

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Package description

Phenopype is a high throughput phenotyping pipeline for Python to support ecologists and evolutionary biologists in extracting high dimensional phenotypic data from digital images. The core feature of this package are high level computer vision functions for image preprocessing, segmentation, and trait measurement that use OpenCV (specifically: the pre-built opencv-python wheels) as a backbone. In addition, Phenopype provides basic project management routines that can automatically organize image data and create customizable analysis-templates (stored in human-readable YAML-format). After finishing a project, users can share or archive the project structure so that anyone can reproduce all collected data with only a few lines of code (suitable for repositories like DRYAD or OSF). Phenopype works most efficiently when used from an Integrated Development Environment (IDE), like Spyder, and requires only minimal Python coding skills.

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, code-reference and tutorials

Detailed installation instructions, along with further resources regarding Python and the OpenCV backbone, as well as the full code reference and a (growing) number of tutorials and feature demonstrations can be found under https://mluerig.github.io/phenopype/.

How to contribute

Phenopype development is an ongoing process and contribution towards making it a more broadly applicable tool is most welcome. This can be in the form of feature requests (e.g. more functions from the OpenCV library) or by reporting bugs via the issue tracker. You can also get in touch with me directly if you have any suggestions for improvement or want to help me making Phenopype better!