A method for automatic segmentation and splitting of hyperspectral images of raspberry plants collected in field conditions

Abstract Hyperspectral imaging is a technology that can be used to monitor plant responses to stress. Hyperspectral images have a full spectrum for each pixel in the image, 400–2500 nm in this case, giving detailed information about the spectral reflectance of the plant. Although this technology has been used in laboratory-based controlled lighting conditions for early detection of plant disease, the transfer of such technology to imaging plants in field conditions presents a number of challenges. These include problems caused by varying light levels and difficulties of separating the target plant from its background. Here we present an automated method that has been developed to segment raspberry plants from the background using a selected spectral ratio combined with edge detection. Graph theory was used to minimise a cost function to detect the continuous boundary between uninteresting plants and the area of interest. The method includes automatic detection of a known reflectance tile which was kept constantly within the field of view for all image scans. A method to split images containing rows of multiple raspberry plants into individual plants was also developed. Validation was carried out by comparison of plant height and density measurements with manually scored values. A reasonable correlation was found between these manual scores and measurements taken from the images (r2 = 0.75 for plant height). These preliminary steps are an essential requirement before detailed spectral analysis of the plants can be achieved

Matrix Factorization as Search ⋆

Abstract. Simplex Volume Maximization (SiVM) exploits distance geometry for e ciently factorizing gigantic matrices. It was proven successful in game, social media, and plant mining. Here, we review the distance geometry approach and argue that it generally suggests to factorize gigantic matrices using search-based instead of optimization techniques. 1 Interpretable Matrix Factorization Many modern data sets are available in form of a real-valued m × n matrix V of rank r ≤ min(m, n). The columns v1,..., vn of such a data matrix encode information about n objects each of which is characterized by m features. Typical examples of objects include text documents, digital images, genomes, stocks, or social groups. Examples of corresponding features are measurements such as term frequency counts, intensity gradient magnitudes, or incidence relations among the nodes of a graph. In most modern settings, the dimensions of the data matrix are large so that it is useful to determine a compressed representation that may be easier to analyze and interpret in light of domain-speci c knowledge

Metro maps of plant disease dynamics-automated mining of differences using hyperspectral images

Understanding the response dynamics of plants to biotic stress is essential to improve management practices and breeding strategies of crops and thus to proceed towards a more sustainable agriculture in the coming decades. In this context, hyperspectral imaging offers a particularly promising approach since it provides non-destructive measurements of plants correlated with internal structure and biochemical compounds. In this paper, we present a cascade of data mining techniques for fast and reliable data-driven sketching of complex hyperspectral dynamics in plant science and plant phenotyping. To achieve this, we build on top of a recent linear time matrix factorization technique, called Simplex Volume Maximization, in order to automatically discover archetypal hyperspectral signatures that are characteristic for particular diseases. The methods were applied on a data set of barley leaves (Hordeum vulgare) diseased with foliar plant pathogens Pyrenophora teres, Puccinia hordei and Blumeria graminis hordei. Towards more intuitive visualizations of plant disease dynamics, we use the archetypal signatures to create structured summaries that are inspired by metro maps, i.e. schematic diagrams of public transport networks. Metro maps of plant disease dynamics produced on several real-world data sets conform to plant physiological knowledge and explicitly illustrate the interaction between diseases and plants. Most importantly, they provide an abstract and interpretable view on plant disease progression

Feeding the world with big data: Uncovering spectral characteristics and dynamics of stressed plants

Modern communication, sensing, and actuator technologies as well as methods from signal processing, pattern recognition, and data mining are increasingly applied in agriculture, ultimately helping to meet the challenge of “How to feed a hungry world?” Developments such as increased mobility, wireless networks, new environmental sensors, robots, and the computational cloud put the vision of a sustainable agriculture for anybody, anytime, and anywhere within reach. Unfortunately, data-driven agriculture also presents unique computational problems in scale and interpretability: (1) Data is gathered often at massive scale, and (2) researchers and experts of complementary skills have to cooperate in order to develop models and tools for data intensive discovery that yield easy-to-interpret insights for users that are not necessarily trained computer scientists

Non-negative factor analysis supporting the interpretation of elemental distribution images acquired by XRF

Stacks of elemental distribution images acquired by XRF can be difficult to interpret, if they contain high degrees of redundancy and components differing in their quantitative but not qualitative elemental composition. Factor analysis, mainly in the form of Principal Component Analysis (PCA), has been used to reduce the level of redundancy and highlight correlations. PCA, however, does not yield physically meaningful representations as they often contain negative values. This limitation can be overcome, by employing factor analysis that is restricted to non-negativity. In this paper we present the first application of the Python Matrix Factorization Module (pymf) on XRF data. This is done in a case study on the painting Saul and David from the studio of Rembrandt van Rijn. We show how the discrimination between two different Co containing compounds with minimum user intervention and a priori knowledge is supported by Non-Negative Matrix Factorization (NMF)