Canopy temperature (CT) has been related to water-use and yield formation in crops. However, constantly (e.g., sun illumination angle, ambient temperature) as well as rapidly (e.g., clouds) changing environmental conditions make it difficult to compare measurements taken even at short time intervals. This poses a great challenge for highthroughput field phenotyping (HTFP). The aim of this study was to i) set up a workflow for unmanned aerial vehicles (UAV) based HTFP of CT, ii) investigate different data processing procedures to combine information from multiple images into orthomosaics, iii) investigate the repeatability of the resulting CT by means of heritability, and iv) investigate the optimal timing for thermography measurements. Additionally, the approach was v) compared with other methods for HTFP of CT. The study was carried out in a winter wheat field trial with 354 genotypes planted in two replications in a temperate climate, where a UAV captured CT in a time series of 24 flights during 6 weeks of the grain-filling phase. Custom-made thermal ground control points enabled accurate georeferencing of the data. The generated thermal orthomosaics had a high spatial accuracy (mean ground sampling distance of 5.03 cm/pixel) and position accuracy [mean root-mean-square deviation (RMSE) = 4.79 cm] over all time points. An analysis on the impact of the measurement geometry revealed a gradient of apparent CT in parallel to the principle plane of the sun and a hotspot around nadir. Averaging information from all available images (and all measurement geometries) for an area of interest provided the best results by means of heritability. Correcting for spatial in-field heterogeneity as well as slight environmental changes during the measurements were performed with the R package SpATS. CT heritability ranged from 0.36 to 0.74. Highest heritability values were found in the early afternoon. Since senescence was found to influence the results, it is recommended to measure CT in wheat after flowering and before the onset of senescence. Overall, lowaltitude and high-resolution remote sensing proved suitable to assess the CT of crop

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The aim of this paper is to map agricultural crops by classifying satellite image time series. Domain experts in agriculture work with crop type labels that are organised in a hierarchical tree structure, where coarse classes (like orchards) are subdivided into finer ones (like apples, pears, vines, etc.). We develop a crop classification method that exploits this expert knowledge and significantly improves the mapping of rare crop types. The three-level label hierarchy is encoded in a convolutional, recurrent neural network (con-vRNN), such that for each pixel the model predicts three labels at different level of granularity. This end-to-end trainable, hierarchical network architecture allows the model to learn joint feature representations of rare classes (e.g., apples, pears) at a coarser level (e.g., orchard ), thereby boosting classification performance at the fine-grained level. Additionally, labelling at different granularity also makes it possible to adjust the output according to the classification scores; as coarser labels with high confidence are sometimes more useful for agricultural practice than fine-grained but very uncertain labels. We validate the proposed method on a new, large dataset that we make public. ZueriCrop covers an area of 50 km × 48 km in the Swiss cantons of Zurich and Thurgau with a total of 116'000 individual fields spanning 48 crop classes, and 28,000 (multi-temporal) image patches from Sentinel-2. We compare our proposed hierarchical convRNN model with several baselines, including methods designed for imbalanced class distributions. The hierarchical approach performs superior by at least 9.9 percentage points in F1-score.

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