Fig. 3.

Image acquisition and analysis workflow. Root growth pouches are opened, and then the plastic film is carefully removed from root system. Subsequently, the pouches are placed inside an imaging tray filled with water. Thereafter, a transparent glass plate is placed on the top of the root system. Plant Root Imaging and Data Analysis (PRIDA)—a Python-based image acquisition and data management software—was used for collecting and storing raw images and project meta-data into a single Hierarchical Data Format (HDF5) file. Root images are cropped to the region of interest and passed through a high-throughput image preprocessing pipeline to segment RSA from the background, which improves root image to noise ratio and trait computations. Cleaned images are analyzed to extract root morphological and architectural traits using a combination of WinRhizo, GiaRoots, and other custom software scripts.