Cotton Chronology: Convolutional Neural Network Enables Single-Plant Senescence Scoring with Temporal Drone Images

Senescence is a degenerative biological process that affects most organisms. Timing of senescence is critical for annual and perennial crops and is associated with yield and quality. Tracking time-series senescence data has previously required expert annotation and can be laborious for large-scale research. Here, a convolutional neural network (CNN) was trained on unoccupied aerial system (UAS, drone) images of individual plants of cotton ( Gossypium hirsutum L.), an early application of single-plant analysis (SPA). Using images from 14 UAS flights capturing most of the senescence window, the CNN achieved 71.4% overall classification accuracy across six senescence categories, with class accuracies ranging between 46.8–89.4% despite large imbalances in numbers of images across classes. For example, the number of images ranged from 109 to 1,129 for the lowest-performing class (80% senesced) to the highest-performing class (fully healthy). The results demonstrate that minimally pre-processed UAS images can enable translatable implementations of high-throughput phenotyping using deep learning methods. This has applications for understanding fundamental plant biology, monitoring orchards and other spaced plantings, plant breeding, and genetic research.