  Quantification of physiological changes in plants can capture different
drought mechanisms and assist in selection of tolerant varieties in a high
throughput manner. In this context, an accurate 3D model of plant canopy
provides a reliable representation for drought stress characterization in
contrast to using 2D images. In this paper, we propose a novel end-to-end
pipeline including 3D reconstruction, segmentation and feature extraction,
leveraging deep neural networks at various stages, for drought stress study. To
overcome the high degree of self-similarities and self-occlusions in plant
canopy, prior knowledge of leaf shape based on features from deep siamese
network are used to construct an accurate 3D model using structure from motion
on wheat plants. The drought stress is characterized with a deep network based
feature aggregation. We compare the proposed methodology on several
descriptors, and show that the network outperforms conventional methods.
