Background: Monitoring the timing of seedling emergence and early development via high-throughput phenotyping with computer vision is a challenging topic of high interest in plant science. While most studies focus on the measurements of leaf area index or detection of specific events such as emergence, little attention has been put on the identification of kinetics of events of early seedling development on a seed to seed basis. Result: Imaging systems screened the whole seedling growth process from the top view. Precise annotation of emergence out of the soil, cotyledon opening, and appearance of first leaf was conducted. This annotated data set served to train deep neural networks. Various strategies to incorporate in neural networks, the prior knowledge of the order of the developmental stages were investigated. Best results were obtained with a deep neural network followed with a long short term memory cell, which achieves more than 90% accuracy of correct detection. Conclusion: This work provides a full pipeline of image processing and machine learning to classify three stages of plant growth plus soil on the different accessions of two species of red clover and alfalfa but which could easily be extended to other crops and other stages of development.

In this article, we assess the interest of the recently introduced multiscale scattering transform for texture classification applied for the first time in plant science. Scattering transform is shown to outperform monoscale approaches (gray-level co-occurrence matrix, local binary patterns) but also multiscale approaches (wavelet decomposition) which do not include combinatory steps. The regime in which scatter transform also outperforms a standard CNN architecture in terms of data-set size is evaluated ( ${10}^4$ instances). An approach on how to optimally design the scatter transform based on energy contrast is provided. This is illustrated on the hard and open problem of weed detection in culture crops of high density from the top view in intensity images. An annotated synthetic data-set available under the form of a data challenge and a simulator are proposed for reproducible science. Scatter transform only trained on synthetic data shows an accuracy of $85\%$ when tested on real data.

In this report we investigate various strategies to boost the performance for leaf segmentation of Arabidopsis thaliana in chlorophyll fluorescent imaging without any manual annotation. Direct conversion of RGB images to gray levels picked from CVPPP challenge or from a virtual Arabidopsis thaliana simulator are tested together with synthetic noisy versions of these. Segmentation performed with a state of the art U-Net convolutional neural network is shown to benefit from these approaches with a Dice coefficient between 0.95 and 0.97 on the segmentation of the border of the leaves. A new annotated dataset of fluorescent images is made available.

Since most computer vision approaches are now driven by machine learning, the current bottleneck is the annotation of images. This time-consuming task is usually performed manually after the acquisition of images. In this article, we assess the value of various egocentric vision approaches in regard to performing joint acquisition and automatic image annotation rather than the conventional two-step process of acquisition followed by manual annotation. This approach is illustrated with apple detection in challenging field conditions. We demonstrate the possibility of high performance in automatic apple segmentation (Dice 0.85), apple counting (88 percent of probability of good detection, and 0.09 true-negative rate), and apple localization (a shift error of fewer than 3 pixels) with eye-tracking systems. This is obtained by simply applying the areas of interest captured by the egocentric devices to standard, non-supervised image segmentation. We especially stress the importance in terms of time of using such eye-tracking devices on head-mounted systems to jointly perform image acquisition and automatic annotation. A gain of time of over 10-fold by comparison with classical image acquisition followed by manual image annotation is demonstrated.

Rapid urbanization is a worldwide critical environmental challenge. With this urban migration soaring, we need to live far more efficiently than we currently do by incorporating the natural world in new and innovative ways. There are a lot of researches on ecological, architectural or aesthetic points of view to address this issue. We present a novel approach to assess the visual impact of vegetation in urban street pedestrian view with the assistance of computer vision metrics. We statistically evaluate the correlations of the amount of vegetation with objective computer vision traits such as Fourier domain, color histogram, and estimated depth from monocular view. We show that increasing vegetation in urban street views breaks the orthogonal symmetries of urban blocks, enriches the color space with fractal-like symmetries and decreases the cues of projective geometry in depth. These uncovered statistical facts are applied to predict the requested amount of vegetation to make urban street views appear like natural images. Interestingly, these amounts are found in accordance with the ecosystemic approach for urban planning. Also, the study opens new questions for the understanding of the link between geometry and depth perception.