RootNav 2.0: Deep Learning for Automatic Navigation of Complex Plant Root Architectures

We present a new image analysis approach that provides fully-automatic extraction of complex root system architectures from a range of plant species in varied imaging setups. Driven by modern deep-learning approaches,RootNav 2.0replaces previously manual and semi-automatic feature extraction with an extremely deep multi-task Convolutional Neural Network architecture. The network has been designed to explicitly combine local pixel information with global scene information in order to accurately segment small root features across high-resolution images. In addition, the network simultaneously locates seeds, and first and second order root tips to drive a search algorithm seeking optimal paths throughout the image, extracting accurate architectures without user interaction. The proposed method is evaluated on images of wheat (Triticum aestivumL.) from a seedling assay. The results are compared with semi-automatic analysis via the originalRootNavtool, demonstrating comparable accuracy, with a 10-fold increase in speed. We then demonstrate the ability of the network to adapt to different plant species via transfer learning, offering similar accuracy when transferred to anArabidopsis thalianaplate assay. We transfer for a final time to images ofBrassica napusfrom a hydroponic assay, and still demonstrate good accuracy despite many fewer training images. The tool outputs root architectures in the widely accepted RSML standard, for which numerous analysis packages exist (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://rootsystemml.github.io/">http://rootsystemml.github.io/</ext-link>), as well as segmentation masks compatible with other automated measurement tools.