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With the threshold for crop growth data collection having been markedly decreased by sensor miniaturization and cost reduction, unmanned aerial vehicle (UAV)-based low-altitude remote sensing has shown remarkable advantages in field phenotyping experiments. However, the requirement of interdisciplinary knowledge and the complexity of the workflow have seriously hindered researchers from extracting plot-level phenotypic data from multisource and multitemporal UAV images. To address these challenges, we developed the Integrated High-Throughput Universal Phenotyping (IHUP) software as a data producer and study accelerator that included 4 functional modules: preprocessing, data extraction, data management, and data analysis. Data extraction and analysis requiring complex and multidisciplinary knowledge were simplified through integrated and automated processing. Within a graphical user interface, users can compute image feature information, structural traits, and vegetation indices (VIs), which are indicators of morphological and biochemical traits, in an integrated and high-throughput manner. To fulfill data requirements for different crops, extraction methods such as Ⅵ calculation formulae can be customized. To demonstrate and test the composition and performance of the software, we conducted case-related rice drought phenotype monitoring experiments. In combination with a rice leaf rolling score predictive model, leaf rolling score, plant height, VIs, fresh weight, and drought weight were efficiently extracted from multiphase continuous monitoring data. Despite the significant impact of image processing during plot clipping on processing efficiency, the software can extract traits from approximately 500 plots/min in most application cases. The software offers a user-friendly graphical user interface and interfaces for customizing or integrating various feature extraction algorithms, thereby significantly reducing barriers for nonexperts. It holds the promise of significantly accelerating data production in UAV phenotyping experiments.
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