A Proposed Methodology to Analyze Plant Growth and Movement from Phenomics Data

The Development of a Stereo Vision System to Study the Nutation Movement of Climbing Plants

Climbing plants, such as common beans (Phaseolus vulgaris L.), exhibit complex motion patterns that have long captivated researchers. In this study, we introduce a stereo vision machine system for the in-depth analysis of the movement of climbing plants, using image processing and computer vision. Our approach involves two synchronized cameras, one lateral to the plant and the other overhead, enabling the simultaneous 2D position tracking of the plant tip. These data are then leveraged to reconstruct the 3D position of the tip. Furthermore, we investigate the impact of external factors, particularly the presence of support structures, on plant movement dynamics. The proposed method is able to extract the position of the tip in 86-98% of cases, achieving an average reprojection error below 4 px, which means an approximate error in the 3D localization of about 0.5 cm. Our method makes it possible to analyze how the plant nutation responds to its environment, offering insights into the interplay between climbing plants and their surroundings.

Growth charts for small sample sizes using unsupervised clustering: Application to canine early growth

Breed-specific growth curves (GCs) are needed for neonatal puppies, but breed-specific data may be insufficient. We investigated an unsupervised clustering methodology for modeling GCs by augmenting breed-specific data with data from breeds having similar growth profiles. Puppy breeds were grouped by median growth profiles (bodyweights between birth and Day 20) using hierarchical clustering on principal components. Median bodyweights for breeds in a cluster were centered to that cluster’s median and used to model cluster GCs by Generalized Additive Models for Location, Shape and Scale. These were centered back to breed growth profiles to produce cluster-scale breed GCs. The accuracy of breed-scale GCs modeled with breed-specific data only and cluster-scale breed GCs were compared when modeled from diminishing sample sizes. A complete dataset of Labrador Retriever bodyweights (birth to Day 20) was split into training (410 puppies) and test (460 puppies) datasets. Cluster-scale breed and breed-scale GCs were modelled from defined sample sizes from the training dataset. Quality criteria were the percentages of observed data in the test dataset outside the target growth centiles of simulations. Accuracy of cluster-scale breed GCs remained consistently high down to sampling sizes of three. They slightly overestimated breed variability, but centile curves were smooth and consistent with breed-scale GCs modeled from the complete Labrador Retriever dataset. At sampling sizes ≤ 20, the quality of breed-scale GCs reduced notably. In conclusion, GCs for neonatal puppies generated using a breed-cluster hybrid methodology can be more satisfactory than GCs at purely the breed level when sample sizes are small.

3DeepM: An Ad Hoc Architecture Based on Deep Learning Methods for Multispectral Image Classification

Current predefined architectures for deep learning are computationally very heavy and use tens of millions of parameters. Thus, computational costs may be prohibitive for many experimental or technological setups. We developed an ad hoc architecture for the classification of multispectral images using deep learning techniques. The architecture, called 3DeepM, is composed of 3D filter banks especially designed for the extraction of spatial-spectral features in multichannel images. The new architecture has been tested on a sample of 12210 multispectral images of seedless table grape varieties: Autumn Royal, Crimson Seedless, Itum4, Itum5 and Itum9. 3DeepM was able to classify 100% of the images and obtained the best overall results in terms of accuracy, number of classes, number of parameters and training time compared to similar work. In addition, this paper presents a flexible and reconfigurable computer vision system designed for the acquisition of multispectral images in the range of 400 nm to 1000 nm. The vision system enabled the creation of the first dataset consisting of 12210 37-channel multispectral images (12 VIS + 25 IR) of five seedless table grape varieties that have been used to validate the 3DeepM architecture. Compared to predefined classification architectures such as AlexNet, ResNet or ad hoc architectures with a very high number of parameters, 3DeepM shows the best classification performance despite using 130-fold fewer parameters than the architecture to which it was compared. 3DeepM can be used in a multitude of applications that use multispectral images, such as remote sensing or medical diagnosis. In addition, the small number of parameters of 3DeepM make it ideal for application in online classification systems aboard autonomous robots or unmanned vehicles.