Evaluation of cotton emergence using UAV-based imagery and deep learning

•Developed near real-time data processing framework for single UAV frames.•Developed a deep learning architecture for effective image data processing.•Evaluated stand count and seedling area autonomously.•Developed an open-source data processing pipeline available to the community. Crop emergence is an important agronomic factor for making field management decisions, such as replanting, that are time-sensitive and need to be made at very early stages. Crop emergence, evaluated using plant population, stand count and uniformity, is conventionally quantified manually, not accurate, and labor and time intensive. Unmanned aerial vehicle (UAV)-based imaging systems are able to scout crop fields rapidly. However, data processing can be too slow to make timely decision making. The goal of this study was to develop a novel image processing method for processing UAV images in nearly real-time. In this study, a UAV imaging system was used to capture RGB image frames of cotton seedlings to evaluate stand count and canopy size. Images were pre-processed to correct distortions, calculate ground sample distance and geo-reference cotton rows in the images. A pre-trained deep learning model, resnet 18, was used to estimate stand count and canopy size of cotton seedlings in each image frame. Results showed that the developed method could estimate stand count accurately with R2 = 0.95 in the test dataset. Similar results were achieved for canopy size with an estimation accuracy of R2 = 0.93 in the test dataset. The processing time for each image frame of 20 M pixels with each crop row geo-referenced was 2.22 s (including 1.80 s for pre-processing), which was more efficient than traditional mosaic-based image processing methods. An open-source automated image-processing framework was developed for cotton emergence evaluation and is available to the community for efficient data processing and analytics.