The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

Automated Image Analysis for the Detection of Benthic Crustaceans and Bacterial Mat Coverage Using the VENUS Undersea Cabled Network

The development and deployment of sensors for undersea cabled observatories is presently biased toward the measurement of habitat variables, while sensor technologies for biological community characterization through species identification and individual counting are less common. The VENUS cabled multisensory network (Vancouver Island, Canada) deploys seafloor camera systems at several sites. Our objective in this study was to implement new automated image analysis protocols for the recognition and counting of benthic decapods (i.e., the galatheid squat lobster, Munida quadrispina), as well as for the evaluation of changes in bacterial mat coverage (i.e., Beggiatoa spp.), using a camera deployed in Saanich Inlet (103 m depth). For the counting of Munida we remotely acquired 100 digital photos at hourly intervals from 2 to 6 December 2009. In the case of bacterial mat coverage estimation, images were taken from 2 to 8 December 2009 at the same time frequency. The automated image analysis protocols for both study cases were created in MatLab 7.1. Automation for Munida counting incorporated the combination of both filtering and background correction (Median- and Top-Hat Filters) with Euclidean Distances (ED) on Red-Green-Blue (RGB) channels. The Scale-Invariant Feature Transform (SIFT) features and Fourier Descriptors (FD) of tracked objects were then extracted. Animal classifications were carried out with the tools of morphometric multivariate statistic (i.e., Partial Least Square Discriminant Analysis; PLSDA) on Mean RGB (RGBv) value for each object and Fourier Descriptors (RGBv+FD) matrices plus SIFT and ED. The SIFT approach returned the better results. Higher percentages of images were correctly classified and lower misclassification errors (an animal is present but not detected) occurred. In contrast, RGBv+FD and ED resulted in a high incidence of records being generated for non-present animals. Bacterial mat coverage was estimated in terms of Percent Coverage and Fractal Dimension. A constant Region of Interest (ROI) was defined and background extraction by a Gaussian Blurring Filter was performed. Image subtraction within ROI was followed by the sum of the RGB channels matrices. Percent Coverage was calculated on the resulting image. Fractal Dimension was estimated using the box-counting method. The images were then resized to a dimension in pixels equal to a power of 2, allowing subdivision into sub-multiple quadrants. In comparisons of manual and automated Percent Coverage and Fractal Dimension estimates, the former showed an overestimation tendency for both parameters. The primary limitations on the automatic analysis of benthic images were habitat variations in sediment texture and water column turbidity. The application of filters for background corrections is a required preliminary step for the efficient recognition of animals and bacterial mat patches

The New Seafloor Observatory (OBSEA) for Remote and Long-Term Coastal Ecosystem Monitoring

A suitable sampling technology to identify species and to estimate population dynamics based on individual counts at different temporal levels in relation to habitat variations is increasingly important for fishery management and biodiversity studies. In the past two decades, as interest in exploring the oceans for valuable resources and in protecting these resources from overexploitation have grown, the number of cabled (permanent) submarine multiparametric platforms with video stations has increased. Prior to the development of seafloor observatories, the majority of autonomous stations were battery powered and stored data locally. The recently installed low-cost, multiparametric, expandable, cabled coastal Seafloor Observatory (OBSEA), located 4 km off of Vilanova i la Gertrú, Barcelona, at a depth of 20 m, is directly connected to a ground station by a telecommunication cable; thus, it is not affected by the limitations associated with previous observation technologies. OBSEA is part of the European Multidisciplinary Seafloor Observatory (EMSO) infrastructure, and its activities are included among the Network of Excellence of the European Seas Observatory NETwork (ESONET). OBSEA enables remote, long-term, and continuous surveys of the local ecosystem by acquiring synchronous multiparametric habitat data and bio-data with the following sensors: Conductivity-Temperature-Depth (CTD) sensors for salinity, temperature, and pressure; Acoustic Doppler Current Profilers (ADCP) for current speed and direction, including a turbidity meter and a fluorometer (for the determination of chlorophyll concentration); a hydrophone; a seismometer; and finally, a video camera for automated image analysis in relation to species classification and tracking. Images can be monitored in real time, and all data can be stored for future studies. In this article, the various components of OBSEA are described, including its hardware (the sensors and the network of marine and land nodes), software (data acquisition, transmission, processing, and storage), and multiparametric measurement (habitat and bio-data time series) capabilities. A one-month multiparametric survey of habitat parameters was conducted during 2009 and 2010 to demonstrate these functions. An automated video image analysis protocol was also developed for fish counting in the water column, a method that can be used with cabled coastal observatories working with still images. Finally, bio-data time series were coupled with data from other oceanographic sensors to demonstrate the utility of OBSEA in studies of ecosystem dynamics

Coastal observatories for monitoring of fish behaviour and their responses to environmental changes

The inclusion of behavioral components in the analysis of a community can be of paramount importance in marine ecology. Diel (i.e., 24-h based), seasonal activity rhythms, or longer durational in behavioral responses can result in shifts in populations, and therefore on measurable abundances. Here, we review the value of developing cabled video observatory technology for the remote, long-term, and high-frequency monitoring of fish and their environments in coastal temperate areas. We provide details on the methodological requirements and constraints for the appropriate measurement of fish behavior over various seasonal scales (24 h, seasonal, annual) with camera systems mounted at fixed observatory locations. We highlight the importance of using marine sensors to simultaneously collect relevant environmental data in parallel to image data acquisition. Here we present multiparametric video, oceanographic, and meteorological data collected from the Mediterranean observatory platform, OBSEA (www.​obsea.​es; 20 m water depth). These data are reviewed in relation to ongoing and future developments of cabled observatory science. Two key approaches for the future improvement of cabled observatory technology are: (1) the application of Artificial Intelligence to aid in the analysis of increasingly large, complex, and highly interrelated biological and environmental data sets, and (2) the development of geographical observational networks to enable the reliable spatial analysis of observed populations over extended distances

Do-it-yourself instruments and data processing methods for developing marine citizen observatories

Water is the most important resource for living on planet Earth, covering more than 70% of its surface. The oceans represent more than 97% of the planet total water and they are where more than the 99.5% of the living beings are concentrated. A great number of ecosystems depend on the health of these oceans; their study and protection are necessary. Large datasets over long periods of time and over wide geographical areas can be required to assess the health of aquatic ecosystems. The funding needed for data collection is considerable and limited, so it is important to look at new cost-effective ways of obtaining and processing marine environmental data. The feasible solution at present is to develop observational infrastructures that may increase significantly the conventional sampling capabilities. In this study we promote to achieve this solution with the implementation of Citizen Observatories, based on volunteer participation. Citizen observatories are platforms that integrate the latest information technologies to digitally connect citizens, improving observation skills for developing a new type of research known as Citizen Science. Citizen science has the potential to increase the knowledge of the environment, and aquatic ecosystems in particular, through the use of people with no specific scientific training to collect and analyze large data sets. We believe that citizen science based tools -open source software coupled with low-cost do-it-yourself hardware- can help to close the gap between science and citizens in the oceanographic field. As the public is actively engaged in the analysis of data, the research also provides a strong avenue for public education. This is the objective of this thesis, to demonstrate how open source software and low-cost do-it-yourself hardware are effectively applied to oceanographic research and how can it develop into citizen science. We analyze four different scenarios where this idea is demonstrated: an example of using open source software for video analysis where lobsters were monitored; a demonstration of using similar video processing techniques on in-situ low-cost do-it-yourself hardware for submarine fauna monitoring; a study using open source machine learning software as a method to improve biological observations; and last but not least, some preliminar results, as proof of concept, of how manual water sampling could be replaced by low-cost do-it-yourself hardware with optical sensors.L’aigua és el recurs més important per la vida al planeta Terra, cobrint més del 70% de la seva superfície. Els oceans representen més del 70% de tota l'aigua del planeta, i és on estan concentrats més del 99.5% dels éssers vius. Un gran nombre d'ecosistemes depenen de la salut d'aquests oceans; el seu estudi i protecció són necessaris. Grans conjunts de dades durant llargs períodes de temps i al llarg d’amples àrees geogràfiques poden ser necessaris per avaluar la salut dels ecosistemes aquàtics. El finançament necessari per aquesta recol·lecció de dades és considerable però limitat, i per tant és important trobar noves formes més rendibles d’obtenir i processar dades mediambientals marines. La solució factible actualment és la de desenvolupar infraestructures observacionals que puguin incrementar significativament les capacitats de mostreig convencionals. En aquest estudi promovem que es pot assolir aquesta solució amb la implementació d’Observatoris Ciutadans, basats en la participació de voluntaris. Els observatoris ciutadans són plataformes que integren les últimes tecnologies de la informació amb ciutadans digitalment connectats, millorant les capacitats d’observació, per desenvolupar un nou tipus de recerca coneguda com a Ciència Ciutadana. La ciència ciutadana té el potencial d’incrementar el coneixement del medi ambient, i dels ecosistemes aquàtics en particular, mitjançant l'ús de persones sense coneixement científic específic per recollir i analitzar grans conjunts de dades. Creiem que les eines basades en ciència ciutadana -programari lliure juntament amb maquinari de baix cost i del tipus "fes-ho tu mateix" (do-it-yourself en anglès)- poden ajudar a apropar la ciència del camp oceanogràfic als ciutadans. A mesura que el gran públic participa activament en l'anàlisi de dades, la recerca esdevé també una nova via d’educació pública. Aquest és l’objectiu d’aquesta tesis, demostrar com el programari lliure i el maquinari de baix cost "fes-ho tu mateix" s’apliquen de forma efectiva a la recerca oceanogràfica i com pot desenvolupar-se cap a ciència ciutadana. Analitzem quatre escenaris diferents on es demostra aquesta idea: un exemple d’ús de programari lliure per anàlisi de vídeos de monitoratge de llagostes; una demostració utilitzant tècniques similars de processat de vídeo en un dispositiu in-situ de baix cost "fes-ho tu mateix" per monitoratge de fauna submarina; un estudi utilitzant programari lliure d’aprenentatge automàtic (machine learning en anglès) com a mètode per millorar observacions biològiques; i finalment uns resultats preliminars, com a prova de la seva viabilitat, de com un mostreig manual de mostres d’aigua podria ser reemplaçat per maquinari de baix cost "fes-ho tu mateix" amb sensors òptics

Do-it-yourself instruments and data processing methods for developing marine citizen observatories

La consulta íntegra de la tesi, inclosos els articles no comunicats públicament per drets d'autor, es pot realitzar prèvia petició a l'Arxiu de la UPCWater is the most important resource for living on planet Earth, covering more than 70% of its surface. The oceans represent more than 97% of the planet total water and they are where more than the 99.5% of the living beings are concentrated. A great number of ecosystems depend on the health of these oceans; their study and protection are necessary. Large datasets over long periods of time and over wide geographical areas can be required to assess the health of aquatic ecosystems. The funding needed for data collection is considerable and limited, so it is important to look at new cost-effective ways of obtaining and processing marine environmental data. The feasible solution at present is to develop observational infrastructures that may increase significantly the conventional sampling capabilities. In this study we promote to achieve this solution with the implementation of Citizen Observatories, based on volunteer participation. Citizen observatories are platforms that integrate the latest information technologies to digitally connect citizens, improving observation skills for developing a new type of research known as Citizen Science. Citizen science has the potential to increase the knowledge of the environment, and aquatic ecosystems in particular, through the use of people with no specific scientific training to collect and analyze large data sets. We believe that citizen science based tools -open source software coupled with low-cost do-it-yourself hardware- can help to close the gap between science and citizens in the oceanographic field. As the public is actively engaged in the analysis of data, the research also provides a strong avenue for public education. This is the objective of this thesis, to demonstrate how open source software and low-cost do-it-yourself hardware are effectively applied to oceanographic research and how can it develop into citizen science. We analyze four different scenarios where this idea is demonstrated: an example of using open source software for video analysis where lobsters were monitored; a demonstration of using similar video processing techniques on in-situ low-cost do-it-yourself hardware for submarine fauna monitoring; a study using open source machine learning software as a method to improve biological observations; and last but not least, some preliminar results, as proof of concept, of how manual water sampling could be replaced by low-cost do-it-yourself hardware with optical sensors.L’aigua és el recurs més important per la vida al planeta Terra, cobrint més del 70% de la seva superfície. Els oceans representen més del 70% de tota l'aigua del planeta, i és on estan concentrats més del 99.5% dels éssers vius. Un gran nombre d'ecosistemes depenen de la salut d'aquests oceans; el seu estudi i protecció són necessaris. Grans conjunts de dades durant llargs períodes de temps i al llarg d’amples àrees geogràfiques poden ser necessaris per avaluar la salut dels ecosistemes aquàtics. El finançament necessari per aquesta recol·lecció de dades és considerable però limitat, i per tant és important trobar noves formes més rendibles d’obtenir i processar dades mediambientals marines. La solució factible actualment és la de desenvolupar infraestructures observacionals que puguin incrementar significativament les capacitats de mostreig convencionals. En aquest estudi promovem que es pot assolir aquesta solució amb la implementació d’Observatoris Ciutadans, basats en la participació de voluntaris. Els observatoris ciutadans són plataformes que integren les últimes tecnologies de la informació amb ciutadans digitalment connectats, millorant les capacitats d’observació, per desenvolupar un nou tipus de recerca coneguda com a Ciència Ciutadana. La ciència ciutadana té el potencial d’incrementar el coneixement del medi ambient, i dels ecosistemes aquàtics en particular, mitjançant l'ús de persones sense coneixement científic específic per recollir i analitzar grans conjunts de dades. Creiem que les eines basades en ciència ciutadana -programari lliure juntament amb maquinari de baix cost i del tipus "fes-ho tu mateix" (do-it-yourself en anglès)- poden ajudar a apropar la ciència del camp oceanogràfic als ciutadans. A mesura que el gran públic participa activament en l'anàlisi de dades, la recerca esdevé també una nova via d’educació pública. Aquest és l’objectiu d’aquesta tesis, demostrar com el programari lliure i el maquinari de baix cost "fes-ho tu mateix" s’apliquen de forma efectiva a la recerca oceanogràfica i com pot desenvolupar-se cap a ciència ciutadana. Analitzem quatre escenaris diferents on es demostra aquesta idea: un exemple d’ús de programari lliure per anàlisi de vídeos de monitoratge de llagostes; una demostració utilitzant tècniques similars de processat de vídeo en un dispositiu in-situ de baix cost "fes-ho tu mateix" per monitoratge de fauna submarina; un estudi utilitzant programari lliure d’aprenentatge automàtic (machine learning en anglès) com a mètode per millorar observacions biològiques; i finalment uns resultats preliminars, com a prova de la seva viabilitat, de com un mostreig manual de mostres d’aigua podria ser reemplaçat per maquinari de baix cost "fes-ho tu mateix" amb sensors òptics.Postprint (published version

From bottom landers to observatory networks

For a long time, deep-sea investigation relied on autonomous bottom landers. Landers can vary in size from 200 kg weight to more than 2 t for the heaviest scientific landers and are used during exploration cruises on medium periods, from one week to some months. Today, new requirements appear. Scientists want to understand in detail the phenomena outlined during exploration cruises, to elaborate a model for future forecasting. For this, it is necessary to deploy instrumentation at a precise location often for a long period. A new mode of ocean science investigation using longterm seafloor observatories to obtain four dimensional data sets has appeared. Although this concept has been proposed for many years, the high level of investment required limits the number of projects implemented. Only multidisciplinary programs, supported by a strong social requirement were funded. Some observatories have been deployed

A Novel Morphometry-Based Protocol of Automated Video-Image Analysis for Species Recognition and Activity Rhythms Monitoring in Deep-Sea Fauna

The understanding of ecosystem dynamics in deep-sea areas is to date limited by technical constraints on sampling repetition. We have elaborated a morphometry-based protocol for automated video-image analysis where animal movement tracking (by frame subtraction) is accompanied by species identification from animals' outlines by Fourier Descriptors and Standard K-Nearest Neighbours methods. One-week footage from a permanent video-station located at 1,100 m depth in Sagami Bay (Central Japan) was analysed. Out of 150,000 frames (1 per 4 s), a subset of 10.000 was analyzed by a trained operator to increase the efficiency of the automated procedure. Error estimation of the automated and trained operator procedure was computed as a measure of protocol performance. Three displacing species were identified as the most recurrent: Zoarcid fishes (eelpouts), red crabs (Paralomis multispina), and snails (Buccinum soyomaruae). Species identification with KNN thresholding produced better results in automated motion detection. Results were discussed assuming that the technological bottleneck is to date deeply conditioning the exploration of the deep-sea

Advancing fishery-independent stock assessments for the Norway lobster (Nephrops norvegicus) with new monitoring technologies

The Norway lobster, Nephrops norvegicus, supports a key European fishery. Stock assessments for this species are mostly based on trawling and UnderWater TeleVision (UWTV) surveys. However, N. norvegicus are burrowing organisms and these survey methods are unable to sample or observe individuals in their burrows. To account for this, UWTV surveys generally assume that "1 burrow system = 1 animal", due to the territorial behavior of N. norvegicus. Nevertheless, this assumption still requires in-situ validation. Here, we outline how to improve the accuracy of current stock assessments for N. norvegicus with novel ecological monitoring technologies, including: robotic fixed and mobile camera-platforms, telemetry, environmental DNA (eDNA), and Artificial Intelligence (AI). First, we outline the present status and threat for overexploitation in N. norvegicus stocks. Then, we discuss how the burrowing behavior of N. norvegicus biases current stock assessment methods. We propose that state-of-the-art stationary and mobile robotic platforms endowed with innovative sensors and complemented with AI tools could be used to count both animals and burrows systems in-situ, as well as to provide key insights into burrowing behavior. Next, we illustrate how multiparametric monitoring can be incorporated into assessments of physiology and burrowing behavior. Finally, we develop a flowchart for the appropriate treatment of multiparametric biological and environmental data required to improve current stock assessment methods

Advancing fishery-independent stock assessments for the Norway lobster (Nephrops norvegicus) with new monitoring techn

The Norway lobster, Nephrops norvegicus, supports a key European fishery. Stock assessments for this species are mostly based on trawling and UnderWater TeleVision (UWTV) surveys. However, N. norvegicus are burrowing organisms and these survey methods are unable to sample or observe individuals in their burrows. To account for this, UWTV surveys generally assume that “1 burrow system = 1 animal”, due to the territorial behavior of N. norvegicus. Nevertheless, this assumption still requires in-situ validation. Here, we outline how to improve the accuracy of current stock assessments for N. norvegicus with novel ecological monitoring technologies, including: robotic fixed and mobile camera-platforms, telemetry, environmental DNA (eDNA), and Artificial Intelligence (AI). First, we outline the present status and threat for overexploitation in N. norvegicus stocks. Then, we discuss how the burrowing behavior of N. norvegicus biases current stock assessment methods. We propose that state-of-the-art stationary and mobile robotic platforms endowed with innovative sensors and complemented with AI tools could be used to count both animals and burrows systems in-situ, as well as to provide key insights into burrowing behavior. Next, we illustrate how multiparametric monitoring can be incorporated into assessments of physiology and burrowing behavior. Finally, we develop a flowchart for the appropriate treatment of multiparametric biological and environmental data required to improve current stock assessment methods