phenopype 1.0.2

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 functions for image processing that can be stacked and executed sequentially to efficiently process single images or large data sets 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 (check the high throughput workflow). Phenopype can be run from Python or from a Python Integrated Development Environment (IDE), like Spyder. Some Python knowledge is necessary, but most of the heavy lifting is done in the background. Phenopype can be installed from the Python Package Index (PYPI) using pip install phenopype. To get started, clone the Github-repo and run the tutorials.

Documentation

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

Installation

https://mluerig.github.io/phenopype/installation ==> pip install phenopype

API-reference

https://mluerig.github.io/phenopype/api ==> overview of currently implemented CV functions

Tutorials

https://mluerig.github.io/phenopype/tutorial_2_phenopype_workflow ==> phenopype has different workflows

Example cases

https://mluerig.github.io/phenopype/example_1_detect_objects_isopods ==> more to be added