Living up to the hype of hyperspectral aquatic remote sensing: science, resources and outlook

Intensifying pressure on global aquatic resources and services due to population growth and climate change is inspiring new surveying technologies to provide science-based information in support of management and policy strategies. One area of rapid development is hyperspectral remote sensing: imaging across the full spectrum of visible and infrared light. Hyperspectral imagery contains more environmentally meaningful information than panchromatic or multispectral imagery and is poised to provide new applications relevant to society, including assessments of aquatic biodiversity, habitats, water quality, and natural and anthropogenic hazards. To aid in these advances, we provide resources relevant to hyperspectral remote sensing in terms of providing the latest reviews, databases, and software available for practitioners in the field. We highlight recent advances in sensor design, modes of deployment, and image analysis techniques that are becoming more widely available to environmental researchers and resource managers alike. Systems recently deployed on space- and airborne platforms are presented, as well as future missions and advances in unoccupied aerial systems (UAS) and autonomous in-water survey methods. These systems will greatly enhance the ability to collect interdisciplinary observations on-demand and in previously inaccessible environments. Looking forward, advances in sensor miniaturization are discussed alongside the incorporation of citizen science, moving toward open and FAIR (findable, accessible, interoperable, and reusable) data. Advances in machine learning and cloud computing allow for exploitation of the full electromagnetic spectrum, and better bridging across the larger scientific community that also includes biogeochemical modelers and climate scientists. These advances will place sophisticated remote sensing capabilities into the hands of individual users and provide on-demand imagery tailored to research and management requirements, as well as provide critical input to marine and climate forecasting systems. The next decade of hyperspectral aquatic remote sensing is on the cusp of revolutionizing the way we assess and monitor aquatic environments and detect changes relevant to global communities

Applications of Unmanned Aerial Systems (UASs) in Hydrology: A Review

In less than two decades, UASs (unmanned aerial systems) have revolutionized the field of hydrology, bridging the gap between traditional satellite observations and ground-based measurements and allowing the limitations of manned aircraft to be overcome. With unparalleled spatial and temporal resolutions and product-tailoring possibilities, UAS are contributing to the acquisition of large volumes of data on water bodies, submerged parameters and their interactions in different hydrological contexts and in inaccessible or hazardous locations. This paper provides a comprehensive review of 122 works on the applications of UASs in surface water and groundwater research with a purpose-oriented approach. Concretely, the review addresses: (i) the current applications of UAS in surface and groundwater studies, (ii) the type of platforms and sensors mainly used in these tasks, (iii) types of products generated from UAS-borne data, (iv) the associated advantages and limitations, and (v) knowledge gaps and future prospects of UASs application in hydrology. The first aim of this review is to serve as a reference or introductory document for all researchers and water managers who are interested in embracing this novel technology. The second aim is to unify in a single document all the possibilities, potential approaches and results obtained by different authors through the implementation of UASs

Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI 2018

The Conference Proceedings are an impressive display of the current scope of Ecological Informatics. Whilst Data Management, Analysis, Synthesis and Forecasting have been lasting popular themes over the past nine biannual ICEI conferences, ICEI 2018 addresses distinctively novel developments in Data Acquisition enabled by cutting edge in situ and remote sensing technology. The here presented ICEI 2018 abstracts captures well current trends and challenges of Ecological Informatics towards: • regional, continental and global sharing of ecological data, • thorough integration of complementing monitoring technologies including DNA-barcoding, • sophisticated pattern recognition by deep learning, • advanced exploration of valuable information in ‘big data’ by means of machine learning and process modelling, • decision-informing solutions for biodiversity conservation and sustainable ecosystem management in light of global changes

Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI 2018

The Conference Proceedings are an impressive display of the current scope of Ecological Informatics. Whilst Data Management, Analysis, Synthesis and Forecasting have been lasting popular themes over the past nine biannual ICEI conferences, ICEI 2018 addresses distinctively novel developments in Data Acquisition enabled by cutting edge in situ and remote sensing technology. The here presented ICEI 2018 abstracts captures well current trends and challenges of Ecological Informatics towards: • regional, continental and global sharing of ecological data, • thorough integration of complementing monitoring technologies including DNA-barcoding, • sophisticated pattern recognition by deep learning, • advanced exploration of valuable information in ‘big data’ by means of machine learning and process modelling, • decision-informing solutions for biodiversity conservation and sustainable ecosystem management in light of global changes

Towards high fidelity mapping of global inland water quality using earth observation data

This body of work aims to contribute advancements towards developing globally applicable water quality retrieval models using Earth Observation data for freshwater systems. Eutrophication and increasing prevalence of potentially toxic algal blooms among global inland water bodies have become a major ecological concersn and require direct attention. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products. This study provides one of the first assessments of the state-ofthe-art for trophic status (chlorophyll-a) retrievals for small water bodies using Sentinel-3 Ocean and Land Color Imager (OLCI). Multiple fieldwork campaigns were undertaken for the collection of common aquatic biogeophysical and bio-optical parameters that were used to validate current atmospheric correction and chlorophyll-a retrieval algorithms. The study highlighted the difficulties of obtaining robust retrieval estimates from a coarse spatial resolution sensor from highly variable eutrophic water bodies. Atmospheric correction remains a difficult challenge to operational freshwater monitoring, however, the study further validated previous work confirming applicability of simple, empirically derived retrieval algorithms using top-of-atmosphere data. The apparent scarcity of paired in-situ optical and biogeophysical data for productive inland waters also hinders our capability to develop and validate robust retrieval algorithms. Radiative transfer modeling was used to fill this gap through the development of a novel synthetic dataset of top-of-atmosphere and bottom-of-atmosphere reflectances, which attempts to encompass the immense natural optical variability present in inland waters. Novel aspects of the synthetic dataset include: 1) physics-based, two-layered, size and type specific phytoplankton IOPs for mixed eukaryotic/cyanobacteria 6 assemblages, 2) calculations of mixed assemblage chl-a fluorescence, 3) modeled phycocyanin concentration derived from assemblage based phycocyanin absorption, 4) and paired sensor-specific TOA reflectances which include optically extreme cases and contribution of green vegetation adjacency. The synthetic bottom-of-atmosphere reflectance spectra were compiled into 13 distinct optical water types similar to those discovered using in-situ data. Inspection showed similar relationships and ranges of concentrations and inherent optical properties of natural waters. This dataset was used to calculate typical surviving water-leaving signal at top-of-atmosphere, as well as first order calculations of the signal-to-noise-ratio (SNR) for the various optical water types, a first for productive inland waters, as well as conduct a sensitivity analysis of cyanobacteria detection from top-of-atmosphere. Finally, the synthetic dataset was used to train and test four state-of-the-art machine learning architectures for multi-parameter retrieval and cross-sensor capability. Initial results provide reliable estimates of water quality parameters and inherent optical properties over a highly dynamic range of water types, at various spectral and spatial sensor resolutions. It is hoped the results of this work incrementally improves inland water Earth observation on multiple aspects of the forward and inverse modelling process, and provides an improvement in our capabilities for routine, global monitoring of inland water quality

Remote sensing of chlorophyll-a in small inland waters

Small inland waters (SIWs) – waterbodies smaller than 100 km2 – are the predominant form of lakes globally, yet they are highly subject to water quality degradation, especially due to harmful algae blooms (HABs). Space-borne remote sensing has proven its capability to detect and map HABs in coastal waters as well as large waterbodies mostly through estimating chlorophyll-a (Chla). However, remote retrieval of near-surface Chla concentration in SIWs is challenging due to adjacency effects in remotely sensed signals and substantial in situ optical interferences of various water constituents. Although various algorithms have been developed or adapted to estimate Chla from moderate-resolution terrestrial missions (~ 10 – 60 m), there remains a need for robust algorithms to retrieve Chla in SIWs. Here, we introduce and evaluate new approaches to retrieve Chla in small lakes in a large lake catchment using Sentinel-2 and Landsat-8 imagery. In situ Chla data used in this study originate from various sources with contrasting measurement methods, ranging from field fluorometry to high-performance liquid chromatography (HPLC). Our analysis revealed that in vivo Chla measurements are not consistent with in vitro measurements, especially in high Chla amounts, and should be calibrated before being fed into retrieval models. Calibrated models based on phycocyanin (PC) fluorescence and environmental factors, such as turbidity, significantly decreased Chla retrieval error and increased the range of reconstructed Chla values. The proposed calibration models were then employed to build a consistent dataset of in situ Chla for Buffalo Pound Lake (BPL) – 30 km length and 1 km width – in the Qu’Appelle River drainage basin, Saskatchewan, Canada. Using this dataset for training and test, support vector regression (SVR) models were developed and reliably retrieved Chla in BPL. SVR models outperformed well-known commonly used retrieval models, namely ocean color (OC3), 2band, 3band, normalized difference chlorophyll index (NDCI), and mixture density networks (MDN) when applied on ~200 matchups extracted from atmospherically-corrected Sentinel-2 data. SVR models also performed well when applied to Landsat-8 data and data processed through various atmospheric correction (AC) processors. The proposed models also suggested good transferability over two optical water types (OWTs) found in BPL. Based on prior evaluations of the models’ transferability over OWTs in BPL, locally trained machine-learning (ML) models were extrapolated for regional retrieval of Chla in the Qu’Appelle River drainage basin. The regional approach was trained on in situ Chla data from BPL and retrieved Chla in other six lakes in the drainage basin. The proposed regional approach outperformed a recently developed global approach (MDN) in terms of accuracy, and showed more applicability than local models given the scarcity of in situ data in most lakes. In addition, ML models, e.g., SVR, performed consistently better than other models when employed in the regional approach. A rare phenomenon of marked blue discoloration of ice and water in winter 2021 in Pasqua Lake, a small lake in Qu’Appelle Watershed, provided an opportunity to assess the regional approaches in estimating chlorophyll-a for waterbodies where enough training data is not available. Therefore, using a developed model based on data from BPL, we produced Chla maps and could successfully relate the discoloration event to a late fall bloom in Pasqua Lake. We included the details of that study in Appendix A. Altogether, the models and approaches introduced in this thesis can serve as first steps toward developing a remote-sensing-based early warning system for monitoring HABs in small inland waters. Results showed that the development of an early warning system for SIWs based on Chla monitoring is currently possible, thanks to advancements in medium-resolution satellite sensors, in situ data collection methods, and machine learning algorithms. However, further steps need to be taken to improve the accuracy and reliability of systems: (a) in situ data need to be consistent for being fed into remote sensing models, (b) retrieval models and AC processors should be improved to provide better estimations of Chla, and (c) regional approaches might be developed as alternatives for local and global approaches in the absence of accurate AC processors and scarcity of in situ Chla data

Remote sensing in shallow lake ecology

Shallow lakes are an important ecological and socio-economic resource. However, the impact of human pressures, both at the lake and catchment scale, has precipitated a decline in the ecological status of many shallow lakes, both in the UK, and throughout Europe. There is now, as direct consequence, unprecedented interest in the assessment and monitoring of ecological status and trajectory in shallow lakes, not least in response to the European Union Water Framework Directive (2000/60/EC). In this context, the spatially-resolving and panoramic data provided by remote sensing platforms may be of immense value in the construction of effective and efficient strategies for the assessment and monitoring of ecological status in shallow lakes and, moreover, in providing new, spatially-explicit, insights into the function of these ecosystems and how they respond to change. This thesis examined the use of remote sensing data for the assessment of (i) phytoplankton abundance and species composition and (ii) aquatic vegetation distribution and ecophysiological status in shallow lakes with a view to establishing the credence of such an approach and its value in limnological research and monitoring activities. High resolution in-situ and airborne remote sensing data was collected during a 2-year sampling campaign in the shallow lakes of the Norfolk Broads. It was demonstrated that semi-empirical algorithms could be formulated and used to provide accurate and robust estimations of the concentration of chlorophyll-a, even in these optically-complex waters. It was further shown that it was possible to differentiate and quantify the abundance of cyanobacteria using the biomarker pigment C-phycocyanin. The subsequent calibration of the imagery obtained from the airborne reconnaissance missions permitted the construction of diurnal and seasonal regional-scale time-series of phytoplankton dynamics in the Norfolk Broads. This approach was able to deliver unique spatial insights into the migratory behaviour of a potentially-toxic cyanobacterial bloom. It was further shown that remote sensing can be used to map the distribution of aquatic plants in shallow lakes, importantly including the extent of submerged vegetation, which is central to the assessment of ecological status. This research theme was subsequently extended in an exploration of the use of remote sensing for assessing the ecophysiological response of wetland plants to nutrient enrichment. It was shown that remote sensing metrics could be constructed for the quantification of plant vigour. The extrapolation of these techniques enabled spatial heterogeneity in the ecophysiological response of Phragmites australis to lake nutrient enrichment to be characterised and assisted the formulation of a mechanistic explanation for the variation in reedswamp performance in these shallow lakes. It is therefore argued that the spatially synoptic data provided by remote sensing has much to offer the assessment, monitoring and policing of ecological status in shallow lakes and, in particular, for facilitating the development of pan-European scale lake surveillance capabilities for the Water Framework Directive (2000/60/EC). It is also suggested that remote sensing can make a valuable contribution to furthering ecological understanding and, most significantly, in enabling ecosystem processes and functions to be examined at the lake-scale

Remote Sensing of the Aquatic Environments

The book highlights recent research efforts in the monitoring of aquatic districts with remote sensing observations and proximal sensing technology integrated with laboratory measurements. Optical satellite imagery gathered at spatial resolutions down to few meters has been used for quantitative estimations of harmful algal bloom extent and Chl-a mapping, as well as winds and currents from SAR acquisitions. The knowledge and understanding gained from this book can be used for the sustainable management of bodies of water across our planet

Spatial variability of aircraft-measured surface energy fluxes in permafrost landscapes

Arctic ecosystems are undergoing a very rapid change due to global warming and their response to climate change has important implications for the global energy budget. Therefore, it is crucial to understand how energy fluxes in the Arctic will respond to any changes in climate related parameters. However, attribution of these responses is challenging because measured fluxes are the sum of multiple processes that respond differently to environmental factors. Here, we present the potential of environmental response functions for quantitatively linking energy flux observations over high latitude permafrost wetlands to environmental drivers in the flux footprints. We used the research aircraft POLAR 5 equipped with a turbulence probe and fast temperature and humidity sensors to measure turbulent energy fluxes along flight tracks across the Alaskan North Slope with the aim to extrapolate the airborne eddy covariance flux measurements from their specific footprint to the entire North Slope. After thorough data pre-processing, wavelet transforms are used to improve spatial discretization of flux observations in order to relate them to biophysically relevant surface properties in the flux footprint. Boosted regression trees are then employed to extract and quantify the functional relationships between the energy fluxes and environmental drivers. Finally, the resulting environmental response functions are used to extrapolate the sensible heat and water vapor exchange over spatio-temporally explicit grids of the Alaskan North Slope. Additionally, simulations from the Weather Research and Forecasting (WRF) model were used to explore the dynamics of the atmospheric boundary layer and to examine results of our extrapolation

Feasibility Study for an Aquatic Ecosystem Earth Observing System Version 1.2.

International audienceMany Earth observing sensors have been designed, built and launched with primary objectives of either terrestrial or ocean remote sensing applications. Often the data from these sensors are also used for freshwater, estuarine and coastal water quality observations, bathymetry and benthic mapping. However, such land and ocean specific sensors are not designed for these complex aquatic environments and consequently are not likely to perform as well as a dedicated sensor would. As a CEOS action, CSIRO and DLR have taken the lead on a feasibility assessment to determine the benefits and technological difficulties of designing an Earth observing satellite mission focused on the biogeochemistry of inland, estuarine, deltaic and near coastal waters as well as mapping macrophytes, macro-algae, sea grasses and coral reefs. These environments need higher spatial resolution than current and planned ocean colour sensors offer and need higher spectral resolution than current and planned land Earth observing sensors offer (with the exception of several R&D type imaging spectrometry satellite missions). The results indicate that a dedicated sensor of (non-oceanic) aquatic ecosystems could be a multispectral sensor with ~26 bands in the 380-780 nm wavelength range for retrieving the aquatic ecosystem variables as well as another 15 spectral bands between 360-380 nm and 780-1400 nm for removing atmospheric and air-water interface effects. These requirements are very close to defining an imaging spectrometer with spectral bands between 360 and 1000 nm (suitable for Si based detectors), possibly augmented by a SWIR imaging spectrometer. In that case the spectral bands would ideally have 5 nm spacing and Full Width Half Maximum (FWHM), although it may be necessary to go to 8 nm wide spectral bands (between 380 to 780nm where the fine spectral features occur -mainly due to photosynthetic or accessory pigments) to obtain enough signal to noise. The spatial resolution of such a global mapping mission would be between ~17 and ~33 m enabling imaging of the vast majority of water bodies (lakes, reservoirs, lagoons, estuaries etc.) larger than 0.2 ha and ~25% of river reaches globally (at ~17 m resolution) whilst maintaining sufficient radiometric resolution