High-throughput phenotyping tools

Python software for high-throughput digital image acquisition, pre-processing, and phenotyping of plant organs.

This software was originally designed to phenotype carrots, as described in this paper.

It makes uses of a standardized image layout to automate image acquisition, utilizing QR codes to handle file management, and features of known physical size to convert pixels to spatial resolution.

The OpenCV library is used to subsequently convert RGB images to binary masks, and measure various physical traits, which can be written to a MongoDB collection, or exported as CSV files. It is now primarily used for phenotyping hazelnuts: https://github.com/shbrainard/hazelnut-phenotyping.

This software was developed in collaboration with Julian Bustamante, a graduate student in the Spalding Lab at the University of Wisconsin-Madison, and Christoph Reimers, inventor of the skateboard trivet.