Detection of leaf structures in close-range hyperspectral images using morphological fusion

Close-range hyperspectral images are a promising source of information in plant biology, in particular, for in vivo study of physiological changes. In this study, we investigate how data fusion can improve the detection of leaf elements by combining pixel reflectance and morphological information. The detection of image regions associated to the leaf structures is the first step toward quantitative analysis on the physical effects that genetic manipulation, disease infections, and environmental conditions have in plants. We tested our fusion approach on Musa acuminata (banana) leaf images and compared its discriminant capability to similar techniques used in remote sensing. Experimental results demonstrate the efficiency of our fusion approach, with significant improvements over some conventional methods

Detection of leaf structures in close-range hyperspectral images using morphological fusion

Close-range hyperspectral images are a promising source of information in plant biology, in particular, for in vivo study of physiological changes. In this study, we investigate how data fusion can improve the detection of leaf elements by combining pixel reflectance and morphological information. The detection of image regions associated to the leaf structures is the first step toward quantitative analysis on the physical effects that genetic manipulation, disease infections, and environmental conditions have in plants. We tested our fusion approach on Musa acuminata (banana) leaf images and compared its discriminant capability to similar techniques used in remote sensing. Experimental results demonstrate the efficiency of our fusion approach, with significant improvements over some conventional methods

Hyperspectral image representation and processing with binary partition trees

The optimal exploitation of the information provided by hyperspectral images requires the development of advanced image processing tools. Therefore, under the title Hyperspectral image representation and Processing with Binary Partition Trees, this PhD thesis proposes the construction and the processing of a new region-based hierarchical hyperspectral image representation: the Binary Partition Tree (BPT). This hierarchical region-based representation can be interpreted as a set of hierarchical regions stored in a tree structure. Hence, the Binary Partition Tree succeeds in presenting: (i) the decomposition of the image in terms of coherent regions and (ii) the inclusion relations of the regions in the scene. Based on region-merging techniques, the construction of BPT is investigated in this work by studying hyperspectral region models and the associated similarity metrics. As a matter of fact, the very high dimensionality and the complexity of the data require the definition of specific region models and similarity measures. Once the BPT is constructed, the fixed tree structure allows implementing efficient and advanced application-dependent techniques on it. The application-dependent processing of BPT is generally implemented through a specific pruning of the tree. Accordingly, some pruning techniques are proposed and discussed according to different applications. This Ph.D is focused in particular on segmentation, object detection and classification of hyperspectral imagery. Experimental results on various hyperspectral data sets demonstrate the interest and the good performances of the BPT representatio

Wavelet-Based Multicomponent Denoising Profile for the Classification of Hyperspectral Images

The high resolution of the hyperspectral remote sensing images available allows the detailed analysis of even small spatial structures. As a consequence, the study of techniques to efficiently extract spatial information is a very active realm. In this paper, we propose a novel denoising wavelet-based profile for the extraction of spatial information that does not require parameters fixed by the user. Over each band obtained by a wavelet-based feature extraction technique, a denoising profile (DP) is built through the recursive application of discrete wavelet transforms followed by a thresholding process. Each component of the DP consists of features reconstructed by recursively applying inverse wavelet transforms to the thresholded coefficients. Several thresholding methods are explored. In order to show the effectiveness of the extended DP (EDP), we propose a classification scheme based on the computation of the EDP and supervised classification by extreme learning machine. The obtained results are compared to other state-of-the-art methods based on profiles in the literature. An additional study of behavior in the presence of added noise is also performed showing the high reliability of the EDP proposedThis work was supported in part by the Consellería de Educación, Universidade e Formación Profesional under Grants GRC2014/008 and ED431C 2018/2019 and the Ministerio de Economía y Empresa, Gobierno de España under Grant TIN2016-76373-P. Both are cofunded by the European Regional Development FundS

A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community

In recent years, deep learning (DL), a re-branding of neural networks (NNs), has risen to the top in numerous areas, namely computer vision (CV), speech recognition, natural language processing, etc. Whereas remote sensing (RS) possesses a number of unique challenges, primarily related to sensors and applications, inevitably RS draws from many of the same theories as CV; e.g., statistics, fusion, and machine learning, to name a few. This means that the RS community should be aware of, if not at the leading edge of, of advancements like DL. Herein, we provide the most comprehensive survey of state-of-the-art RS DL research. We also review recent new developments in the DL field that can be used in DL for RS. Namely, we focus on theories, tools and challenges for the RS community. Specifically, we focus on unsolved challenges and opportunities as it relates to (i) inadequate data sets, (ii) human-understandable solutions for modelling physical phenomena, (iii) Big Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and learning algorithms for spectral, spatial and temporal data, (vi) transfer learning, (vii) an improved theoretical understanding of DL systems, (viii) high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote Sensin

Remote detection of invasive alien species

The spread of invasive alien species (IAS) is recognized as the most severe threat to biodiversity outside of climate change and anthropogenic habitat destruction. IAS negatively impact ecosystems, local economies, and residents. They are especially problematic because once established, they give rise to positive feedbacks, increasing the likelihood of further invasions and spread. The integration of remote sensing (RS) to the study of invasion, in addition to contributing to our understanding of invasion processes and impacts to biodiversity, has enabled managers to monitor invasions and predict the spread of IAS, thus supporting biodiversity conservation and management action. This chapter focuses on RS capabilities to detect and monitor invasive plant species across terrestrial, riparian, aquatic, and human-modified ecosystems. All of these environments have unique species assemblages and their own optimal methodology for effective detection and mapping, which we discuss in detail

A Low-cost Depth Imaging Mobile Platform for Canola Phenotyping

To meet the high demand for supporting and accelerating progress in the breeding of novel traits, plant scientists and breeders have to measure a large number of plants and their characteristics accurately. A variety of imaging methodologies are being deployed to acquire data for quantitative studies of complex traits. When applied to a large number of plants such as canola plants, however, a complete three-dimensional (3D) model is time-consuming and expensive for high-throughput phenotyping with an enormous amount of data. In some contexts, a full rebuild of entire plants may not be necessary. In recent years, many 3D plan phenotyping techniques with high cost and large-scale facilities have been introduced to extract plant phenotypic traits, but these applications may be affected by limited research budgets and cross environments. This thesis proposed a low-cost depth and high-throughput phenotyping mobile platform to measure canola plant traits in cross environments. Methods included detecting and counting canola branches and seedpods, monitoring canola growth stages, and fusing color images to improve images resolution and achieve higher accuracy. Canola plant traits were examined in both controlled environment and field scenarios. These methodologies were enhanced by different imaging techniques. Results revealed that this phenotyping mobile platform can be used to investigate canola plant traits in cross environments with high accuracy. The results also show that algorithms for counting canola branches and seedpods enable crop researchers to analyze the relationship between canola genotypes and phenotypes and estimate crop yields. In addition to counting algorithms, fusing techniques can be helpful for plant breeders with more comfortable access plant characteristics by improving the definition and resolution of color images. These findings add value to the automation, low-cost depth and high-throughput phenotyping for canola plants. These findings also contribute a novel multi-focus image fusion that exhibits a competitive performance with outperforms some other state-of-the-art methods based on the visual saliency maps and gradient domain fast guided filter. This proposed platform and counting algorithms can be applied to not only canola plants but also other closely related species. The proposed fusing technique can be extended to other fields, such as remote sensing and medical image fusion

Remote Sensing of Plant Biodiversity

At last, here it is. For some time now, the world has needed a text providing both a new theoretical foundation and practical guidance on how to approach the challenge of biodiversity decline in the Anthropocene. This is a global challenge demanding global approaches to understand its scope and implications. Until recently, we have simply lacked the tools to do so. We are now entering an era in which we can realistically begin to understand and monitor the multidimensional phenomenon of biodiversity at a planetary scale. This era builds upon three centuries of scientific research on biodiversity at site to landscape levels, augmented over the past two decades by airborne research platforms carrying spectrometers, lidars, and radars for larger-scale observations. Emerging international networks of fine-grain in-situ biodiversity observations complemented by space-based sensors offering coarser-grain imagery—but global coverage—of ecosystem composition, function, and structure together provide the information necessary to monitor and track change in biodiversity globally. This book is a road map on how to observe and interpret terrestrial biodiversity across scales through plants—primary producers and the foundation of the trophic pyramid. It honors the fact that biodiversity exists across different dimensions, including both phylogenetic and functional. Then, it relates these aspects of biodiversity to another dimension, the spectral diversity captured by remote sensing instruments operating at scales from leaf to canopy to biome. The biodiversity community has needed a Rosetta Stone to translate between the language of satellite remote sensing and its resulting spectral diversity and the languages of those exploring the phylogenetic diversity and functional trait diversity of life on Earth. By assembling the vital translation, this volume has globalized our ability to track biodiversity state and change. Thus, a global problem meets a key component of the global solution. The editors have cleverly built the book in three parts. Part 1 addresses the theory behind the remote sensing of terrestrial plant biodiversity: why spectral diversity relates to plant functional traits and phylogenetic diversity. Starting with first principles, it connects plant biochemistry, physiology, and macroecology to remotely sensed spectra and explores the processes behind the patterns we observe. Examples from the field demonstrate the rising synthesis of multiple disciplines to create a new cross-spatial and spectral science of biodiversity. Part 2 discusses how to implement this evolving science. It focuses on the plethora of novel in-situ, airborne, and spaceborne Earth observation tools currently and soon to be available while also incorporating the ways of actually making biodiversity measurements with these tools. It includes instructions for organizing and conducting a field campaign. Throughout, there is a focus on the burgeoning field of imaging spectroscopy, which is revolutionizing our ability to characterize life remotely. Part 3 takes on an overarching issue for any effort to globalize biodiversity observations, the issue of scale. It addresses scale from two perspectives. The first is that of combining observations across varying spatial, temporal, and spectral resolutions for better understanding—that is, what scales and how. This is an area of ongoing research driven by a confluence of innovations in observation systems and rising computational capacity. The second is the organizational side of the scaling challenge. It explores existing frameworks for integrating multi-scale observations within global networks. The focus here is on what practical steps can be taken to organize multi-scale data and what is already happening in this regard. These frameworks include essential biodiversity variables and the Group on Earth Observations Biodiversity Observation Network (GEO BON). This book constitutes an end-to-end guide uniting the latest in research and techniques to cover the theory and practice of the remote sensing of plant biodiversity. In putting it together, the editors and their coauthors, all preeminent in their fields, have done a great service for those seeking to understand and conserve life on Earth—just when we need it most. For if the world is ever to construct a coordinated response to the planetwide crisis of biodiversity loss, it must first assemble adequate—and global—measures of what we are losing