Integrating spectral and morphological plant features with decision-tree models for early-season cotton biomass and nitrogen status estimation from multi-year UAV data
Authors: Vaishali Swaminathan, Nithya Rajan, J Alex Thomasson, Amrit Shrestha, Karem Meza Capcha, Robert Hardin, Pramod Pokhrel
Abstract
Precision nitrogen (N) management (PNM) for cotton requires in-season monitoring of crop growth parameters and N status indicators to decide fertilizer timing, placement, and application rates for optimal canopy development and yield. This study developed remote sensing and machine learning-based methods to estimate cotton dry biomass weight (DBW), plant N uptake (PNU), plant N concentration (PNC), critical N dilution (Nc), and nitrogen nutrition index (NNI) to support PNM. To achieve this, a three-year field-based N-management study was conducted and unmanned aerial vehicle (UAV)-based multispectral images were acquired between early vegetative growth and flowering stages, critical for fertilizer applications. Spatiotemporally consistent spectral and morphological plant features, including plant height (PH) and fractional canopy cover (FCC), provided reliable model training inputs. DBW, PNU, and PNC estimates from simple regression using vegetation indices (VIs), multiple linear regression (MLR) combining VIs, PH, and FCC, and decision-tree models, random forest regression (RFR) and extreme gradient boosting (XGB), combining spectral reflectance, PH, and FCC were evaluated using trial-held-out (THO) and leave-one-year-out (LOYO) validation methods. The best validation accuracies were from RFRTHO (R2 = 0.88 and MAPE = 23.14% for DBW; R2 = 0.84 and MAPE = 20.61% for PNU; R2 = 0.85 and MAPE = 7.82% for PNC) and XGBTHO (R2 = 0.87 and MAPE = 21.91% for DBW; R2 = 0.81 and MAPE = 21.40% for PNU; R2 = 0.86 and MAPE = 7.66% for PNC). Nc was calculated from model estimated DBW and PNC for high-yielding, medium-to-tall cotton varieties grown in the Texas Coastal Plains and validated using ground-truth biomass measurements. NNI derived from XGBTHO outputs performed marginally better than NNI from RFRTHO in identifying N-deficient plots and multi-level N-stress categorization.
Accurate estimation of forest biomass, a major carbon sink, relies heavily on tree-level traits such as height and species. Unoccupied Aerial Vehicles (UAVs) capturing high-resolution imagery from a single RGB camera offer a cost-effective and scalable approach for mapping and measuring individual trees. We introduce BIRCH-Trees, the first benchmark for individual tree height and species estimation from tree-centered UAV images, spanning three datasets: temperate forests, tropical forests, and boreal plantations. We also present DINOvTree, a unified approach using a Vision Foundation Model (VFM) backbone with task-specific heads for simultaneous height and species prediction. Through extensive evaluations on BIRCH-Trees, we compare DINOvTree against commonly used vision methods, including VFMs, as well as biological allometric equations. We find that DINOvTree achieves top overall results with accurate height predictions and competitive classification accuracy while using only 54% to 58% of the parameters of the second-best approach.
Jannik Endres, Etienne Laliberté, David Rolnick +1
Precision agriculture requires the estimation of plant growth stages in real-time. When the plant growth stage is known, the wastage of resources in cultivation, such as nutrients and water, is reduced as only the required resources need to be supplied. Plants at different growth stages, however, have similar morphological features, which can make autonomous growth stage estimation difficult. This paper presents two feature extraction methods for growth stage estimation: one that uses a bank of Gabor filters and morphological operations, and the other that uses pre-trained convolutional neural networks (CNNs) and transfer learning. We test these methods on a publicly available plant growth stage dataset (bccr-segset) for two species, canola and radish, grown and captured under indoor conditions. The two proposed feature extraction methods are compared, using support vector machines and boosted trees as classifiers. We find that both methods are suitable for real-time applications, and that CNN features outperform the hand-crafted features, both with regard to speed and accuracy. The best system (VGG-19 features, classified with a radial basis function support vector machine) obtained an accuracy of 98.4% for both species, processing an image in 0.08 seconds.
Simbarashe Aldrin Ngorima, Albert Helberg, Marelie H. Davel
In this study, UAV multispectral imagery is used to segment the severity of bacterial leaf blight (BLB) in rice using convolutional neural networks (CNNs) and transformer-based models. The evaluated architectures include U-Net with a ResNet- 101 encoder, U-Net++ with EfficientNet-B3 and EfficientNetB7, DeepLabV3+, and SegFormer, all trained under a common pipeline with three input configurations (multispectral only, multispectral+NDVI, and multispectral+NDRE). Experiments are conducted using the publicly available BLB dataset with performance reported using mean IoU (mIoU), mean F1 (mF1), mean accuracy (mAcc), precision, and recall. U-Net++ with EfficientNet-B3 achieved the highest performance, with an mIoU of 97.62%. SegFormer obtained lower segmentation accuracy but comparable inference speed. Overall, the results indicate that lightweight CNN backbones remain more reliable for operational BLB monitoring while integration of vegetation indices provides small and consistent improvements. The study also highlights the value of standardised UAV datasets to compare disease mapping methods and encourages the use of CNN architectures for field implementation.