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42 results for “marine monitoring”

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zenodo44/100

Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats - Datasets and supporting files

The supporting datasets, scripts, and supplementary information for the manuscript, "Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats," are available within this repository. We conduct an analysis on the coverage of protected areas that cover six threatened marine and coastal and developed two indexes, the Local Proportion of Habitat Protected Index and the Global Proportion of Habitat Protected Index, describing the protection of these habitats locally and globally. The habitats considered are the following: cold corals, warm water corals, knolls and seamounts, mangroves, saltmarshes, and seagrasses. The index scores of each jurisdiction are made available for download in the dataset: habitat_protection_indexes_average.csv The habitat specific index scores for each jurisdiction are made available for download in the dataset: habitat_protection_indexes.csv.  Column name descriptions are available in the text file: Column_name_descriptions_20220301 The scripts used to run the workflow to calculate the indexes, create figures, and calculate statistics for the manuscript are also included. The script 01_Workflow sources the first 9 scripts in the scripts folder to calculate the indexes which relies on the functions script within the functions folder. The rest of the scripts in the folder create the figures and calculate the statistics for the manuscript. A readme pdf file is included here to ease with reproducing the workflow, but we strongly suggest to please visit our github (<a href="https://github.com/jkumagai96/Marine_Habitat_protection">https://github.com/jkumagai96/Marine_Habitat_protection</a>) to reproduce the entire calculation where we provide detailed information on how to run the workflow and package management.

opencc-by-4.0Jun 2021View details →

zenodo44/100

Short-term Monitoring of Coral Reef Marine Protected Areas (MPAs) in the Municipality of Liloan, Central Visayas, Philippines

This is a sampling-event dataset of the short-term monitoring of Poblacion and Kadurong Reefs, two of the marine protected areas Municipality of Liloan, Cebu, Philippines. Water quality and ecological assessments were carried out to monitor the status and trends of biological and physical parameters associated with coral reefs using the standard protocols for surveying tropical marine resources. Specifically, the following measurements were conducted: (1) physico-chemical parameters, (2) phytoplankton and zooplankton occurrence and abundance, (3) fish occurrence and density, and (4) percent cover of benthic components of coral reef. The data can serve as the basis for the formulation and implementation of relevant measures for conservation and protection management of the Poblacion and Kadurong Reefs in Liloan, Cebu, Philippines. In this version, occurrence.csv was revised as described below: <ul> <li>taxonID for Abudefduf vaigiensis (Quoy & Gaimard, 1825) and  Hemiaulus P.A.C. Heiberg, 1863  were corrected.</li> <li>Author names with corrupted characters/symbols were corrected. </li> </ul>

opencc-by-4.0Jul 2021View details →

zenodo44/100

Monitoring NBS for coastal erosion and marine flooding: the Emilia-Romagna case study

The study was conducted in the context of the OPERANDUM project which is an H2020 project which aims at providing tools and methodologies for the assessment of NBS efficiency around the world. As NBS will be tested an artificial dune built with natural materials.  The artificial dune is an engineered structure that will mimic the functioning of natural dunes. Its aims are reducing both natural dune erosion and flooding in adjacent coastal lowlands. It consists of a barrier between the sea and land, in a similar way to a seawall. Unlike the latter, the NBS are ‘dynamic’, i.e. the dune/beach system interacts a great deal and is constantly undergoing small adjustments in response to changes in wind and wave climate or sea level.  Its construction involves the placement of sediment from dredged sources on the beach and it will be reinforced with  a structure composed of biodegradable material. Different typologies of experimental solutions are foreseen. The Bellocchio Beach at Lido di Spina (Italy) was initially chosen for the study, however the Volano beach was selected as the new study area because of the strong erosion caused by an intense storm event in December 2020 at Bellocchio. The dune was built on the Volano beach and monitoring surveys were carried out on this new site.  A morphological monitoring aimed to assess the beach evolution and the performance of the NBS were performed. Monitoring of morphology evolution of shoreline and inland area provide information about impact of the NBS on coastal erosion.  Furthermore, the changes in the form of the work give information about the resistance of the NBS to wave attacks.  Sedimentological campaigns have been planned in order to provide information regarding the texture of the sediments present in the area detected and possibly highlight changes after the construction of the dune. Three monitoring campaigns were carried out before, immediately after and six months later the construction of the dune (January, May and October 2022). All data were analysed to assess local coastal dynamics and NBS evolution. The monitoring consisted of: <ul> <li> topographic and bathymetric surveys (GNSS and multibeam/singlebeam echosounder) to generate DTMs of the entire area (10 m cell size); </li> <li> aerial photogrammetric surveys by UAV for the production of orthophotos and high resolutions DTMs of the emerged beach (1m cell size) and of the dune area (0.2 m cell size); </li> <li> sediment sampling and grain size analysis.  </li> </ul> Surveys show that morphological and sedimentological changes are determined mostly by anthropic actions to the beach and seabed maintenance (artificial winter banks and Sacca di Goro channel). Regarding the dune area no significant changes in morphology were observed due to the limited period between the surveys. Appreciable signals were detected, such as the natural recolonization by pioneer plant species and the slight sand accumulation on the dune foot. This dataset consists of data related to monitoring activities.

opencc-by-4.0Nov 2022View details →

zenodo40/100

SeaPaCS graphic elaboration of the Protocol for marine micro-plastic collection and monitoring in citizen science and for building a L.A.D.I. trawling tool

This  is a graphic elaboration  (in Italian) of the protocol "SeaPaCS deliverable - protocol for plastic monitoring in citizen science" in English and Italian is a deliverable of the SeaPaCS project (Participatory Citizen Science Against Marine Pollution), funded by IMPETUS (project ID 101058677). The protocol  and the visual elaboration has been freely adapted from "LADI and the Trawl" by Coco Coyle with Melissa Novaceski, Emily Wells and Max Liboiron, as published by the Civic Laboratory for Environmental Action Research, August 2016.  The graphic elaboration (as the protocol) in both languages, consists of three parts: 1) how to build a DIY low cost manta trawl device (LADI - Low-Tech Aquatic Detection Debris Instrument) to monitor plastic pollution,  adjusted to materials availability and costs in Italy; 2) how to monitor (the sampling itself and towing procedure); and 3) how to categorize plastic debris back on land.

opencc-by-4.0Nov 2023View details →

dryad40/100

Acoustic features as a tool to visualize and explore marine soundscapes: Applications illustrated using marine mammal Passive Acoustic Monitoring datasets

Passive Acoustic Monitoring (PAM) is emerging as a solution for monitoring species and environmental change over large spatial and temporal scales. However, drawing rigorous conclusions based on acoustic recordings is challenging, as there is no consensus over which approaches, and indices are best suited for characterizing marine and terrestrial acoustic environments. Here, we describe the application of multiple machine-learning techniques to the analysis of a large PAM dataset. We combine pre-trained acoustic classification models (VGGish, NOAA & Google Humpback Whale Detector), dimensionality reduction (UMAP), and balanced random forest algorithms to demonstrate how machine-learned acoustic features capture different aspects of the marine environment. The UMAP dimensions derived from VGGish acoustic features exhibited good performance in separating marine mammal vocalizations according to species and locations. RF models trained on the acoustic features performed well for labelled sounds in the 8 kHz range, however, low and high-frequency sounds could not be classified using this approach. The workflow presented here shows how acoustic feature extraction, visualization, and analysis allow for establishing a link between ecologically relevant information and PAM recordings at multiple scales. The datasets and scripts provided in this repository allow replicating the results presented in the publication.

opencc-zeroFeb 2024View details →

zenodo40/100

Biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring

These are the raw sequencing data and associated analysis codes for the study of "biofouling sponges as natural eDNA samplers for marine vertebrate biodiversity monitoring".

opencc-by-4.0Nov 2023View details →

zenodo40/100

Surface Marine Carbonate System Data (2019-2024) from Volunteer Observing Ship monitoring across the Western Mediterranean Sea

1.     Introduction We present here a high-resolution dataset which spans five years (February 2019 - February 2024) and is based on weekly physicochemical observations of the surface waters along the western boundary of the Mediterranean Sea. Data were automatically collected by a Surface Ocean Observation Platform (SOOP) operating in underway mode aboard the Volunteer Observing Ship (VOS) MV JONA SOPHIE (formerly RENATE P until November 2021), a container ship managed by Nisa Maritima on the route between the Canary Islands and Barcelona. A total of 92 routes were completed in the Mediterranean Sea during the observation period. The SOOP CanOA-VOS line, designed and maintained by the QUIMA research group at IOCAG-ULPGC, is part of Spain’s contribution to the Integrated Carbon Observation System (ICOS-ERIC) since 2021 and is recognized as an ICOS Class 1 Ocean Station, ensuring that the measurement equipment and data collection techniques meet ICOS-ERIC's high-quality standards and methodological recommendations. The data collected is also available at the ICOS Data Portal (<a href="https://www.icos-cp.eu/data-products/ocean-release">https://www.icos-cp.eu/data-products/ocean-release</a>). 2.     Data collection The dataset includes continuous monitoring of CO2 levels in both surface ocean and low atmosphere, following protocols to ensure data comparability and quality given by Pierrot et al., (2009). A detailed description is provided by Curbelo-Hernández et al., 2021a, 2021b). An automated CO2 molar fraction (xCO2) measurement system, developed by Craig Nail and commercialized by General Oceanics™, was installed on the ship. This system integrates air and seawater equilibrators with a non-dispersive infrared analyzer by LICOR® for xCO2 detection. The analyzer is regularly calibrated using standard gases provided by the NOAA, traceable to the World Meteorological Organization (WMO). They were in the order of 0 ppm, 250 ppm, 400 ppm and 550 ppm until January 2021, when the gas bottles for standard 2 to 4 were changed for a new set with concentrations in the order of 300 ppm, 500 ppm and 800 ppm. In addition to xCO2, sea surface temperature (SST) and sea surface salinity (SSS) were monitored using high-precision instruments. The SST was monitored by using a SBE38 thermometer placed at the main seawater intake in the engine room, with a reported error of ±0.01ºC. A SBE45 thermosalinograph and a Hart Scientific HT1523 Handheld Thermometer, with reported errors of ±0.01ºC, were used to monitor the temperature at the entrance of the wet box and inside the equilibrator, respectively. The SBE45 thermosalinograph measured the sea surface salinity (SSS) with an estimated error of ±0.005. Discrete seawater samples were also collected during three round trips in February 2020, March 2021, and October 2023, for further analysis of total alkalinity and dissolved inorganic carbon. A total of 102 discrete samples has been collected in the Mediterranean Sea. Total alkalinity (AT) and total inorganic carbon (CT) were determined using a VINDTA 3C according to Mintrop et al., 2000. AT was analyzed via potentiometric titration with HCl, following the carbonic acid endpoint method (Millero et al., 1993; Dickson and Goyet, 1994), while CT was determined through coulometric titration (Johnson et al., 1993). The VINDTA 3C was calibrated using Certified Reference Material (CRMs) by A. Dickson, ensuring an accuracy of ±1.5 μmol kg-1 for AT and ±1.0 μmol kg-1 for CT. The dataset contains some gaps, including a year-long gap from September 2021 to 2022 due to vessel maintenance and shorter gaps due to technical issues, which were addressed during routine maintenance. Some technical issues in 2020 were delayed due to COVID-19 constraints. 3. Dataset content The dataset includes the following variables:  ·       “Date” (dd/mm/yyyy) ·       “Time” (hh:mm:ss) ·       “Latitude” ·       “Longitude” ·       “equTemp”: seawater temperature measured inside the equilibrator using a Hart Scientific HT1523 Handheld Thermometer. ·       “stdVal”: value of the standard gases used for automatically calibrations. ·       “xCO2”: measured CO2 molar fraction without performing any correlation (raw data). ·       “atmPress”: Atmospheric pressure (units: atm). ·       “equPress”: Diffeence in pressure between the atmosphere and the equilibrator (units: atm). ·       “SST_SBE38”: Sea surface temperature measured with a SBE38 thermometer at the main seawater intake of the vessel. ·       “Temp_SBE45”: Seawater temperature measured with a SBE45 thermosalinograph just before the water supply to the equilibrator. ·       “SSS_SBE45”: Sea surface salinity measured with a SBE45 thermosalinograph just before the water supply to the equilibrator. ·       “xCO2corr_sw”: CO2 molar fraction measured in the sea surface after correction by using standard gases. ·       “xCO2corr_atm”: CO2 molar fraction measured in low atmosphere after correction by using standard gases. ·       “pCO2sw”: Partial pressure of CO2 in the sea surface (units: µatm). ·       “pCO2atm”: Partial pressure of CO2 in low atmosphere (units: µatm). ·       “fCO2sw”: fugacity of CO2 in the sea surface (units: µatm). ·       “fCO2atm”: fugacity of CO2 in low atmosphere (units: µatm). ·       “AT”: Total Alkalinity (µmol kg-1) ·       “CT”: Total Inorganic Carbon (µmol kg-1) ·       “pH”: pH in surface seawater at in situ temperature computed in CO2sys using as input variables AT and fCO2sw. ·       “pH25”: pH in surface seawater at constant temperature of 25ºC computed in CO2sys using as input variables AT and fCO2sw.   Acknowledgement This research was supported by the Canary Islands Government and the Loro Parque Foundation through the CanBIO project, CanOA subproject (2019–2024), and the CARBOCAN agreement (Consejería de Transición Ecológica y Energía, Gobierno de Canarias). We would like to thank the JONA SOPHIE ship owner, the NISA-Marítima company and the captains and crew members for the support during this collaboration. Special thanks to the technician Adrian Castro-Alamo for biweekly equipment maintenance and discrete sampling of total alkalinity aboard the ship. The SOOP CanOA-VOS line is part of the Spanish contribution to the Integrated Carbon Observation System (ICOS-ERIC; https://www.icos-cp.eu/) since 2021 and has been recognized as an ICOS Class 1 Ocean Station. The participation of D. C-H was funded by the PhD grant PIFULPGC-2020-2 ARTHUM-2

opencc-by-4.0Aug 2024View details →

dryad40/100

Acoustic features as a tool to visualize and explore marine soundscapes: Applications illustrated using marine mammal Passive Acoustic Monitoring datasets

Open the record for dataset details and reuse information.

publicFeb 2024View details →

dryad40/100

Data from: Estimating a physiologically-based threshold to oxygen and temperature from marine monitoring data reveals challenges and opportunities for forecasting distribution shifts

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publicNov 2024View details →

dryad40/100

Gaps in DNA sequence libraries for Macaronesian marine macroinvertebrates imply decades till completion and robust monitoring

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publicMay 2021View details →

dryad36/100

Data from: environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: towards a baseline for biodiversity monitoring of unexplored marine habitats

Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from nineteen genera of fish, six of these have also been observed on towed underwater videos, while thirteen were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.

opencc-zeroFeb 2024View details →

dryad36/100

Data from: Monitoring temporal and spatial trends of illegal and legal fishing in Canada's marine conservation areas using vessel tracking datasets

Expansion of marine conservation areas (CA) necessitates resource-efficient and achievable strategies for monitoring and evaluation of ongoing fishing activity at national levels. To demonstrate and explore such a strategy, we conducted the first extensive analysis of fishing activity within Canada's static, geographically defined marine CAs with fishing regulations (n = 264 areas). We used eight years of Automatic Identification System data to estimate fishing effort across three oceans and conducted temporal and spatial comparisons specific to each CA's regulations and enactment date. We addressed questions on CA effectiveness, fishing displacement, fishing the line behavior, and relationships between fishing activity and spatial CA attributes. We estimated 22,000 hours of fishing activity within CAs after enactments, 22% of which was identified as illegal. CA effectiveness appeared to be lowest for Atlantic CAs based on illegal fishing effort density within CAs. Fishing displacement and fishing the line was generally not apparent as buffer areas around CAs tended to already have higher fishing effort prior to enactments. CA effectiveness and responses to CAs varied considerably, as was visualized using timeseries plots and maps developed for each CA. Our evaluation of a nation's full suite of CAs provides managers with a foundation and approach for continued monitoring and reporting.

opencc-zeroMar 2023View details →

zenodo36/100

Supplementary Files: "Improved baited remote underwater video (BRUV) for 24h re-al-time monitoring of surface and deep-sea marine species"

In the supplementary material you will find: Figure S1: Photographs of the different parts of the innovative BRUV design; Video S1: Video footage of a bluntnose sixgill shark; Video S2: Types of markings in blue sharks bodies to identify individuals; Video S3: Other marine pelagic species.

opencc-by-4.0Apr 2023View details →

dryad36/100

Data from: Multi-tool marine metabarcoding bioassessment for baselining and monitoring species and communities in kelp habitats

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publicJul 2025View details →

dryad36/100

Data from: Monitoring temporal and spatial trends of illegal and legal fishing in Canada's marine conservation areas using vessel tracking datasets

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publicNov 2024View details →

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Data from: environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: towards a baseline for biodiversity monitoring of unexplored marine habitats

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publicFeb 2024View details →

dryad36/100

Data from: The core of the matter – Importance of identification method and biological replication for benthic marine monitoring

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publicNov 2024View details →

dryad32/100

Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

1. Reliable and accurate biodiversity census methods are essential for monitoring ecosystem health and assessing potential ecological impacts of future development projects. Although metabarcoding is increasingly used to study biodiversity across ecological research, morphology-based identification remains the preferred approach for marine ecological impact assessments. Comparing metabarcoding to morphology-based protocols currently used by ecological surveyors is essential to determine whether this DNA-based approach is suitable for the long-term monitoring of marine ecosystems. 2. We compared metabarcoding and morphology-based approaches for the analysis of invertebrates in low diversity intertidal marine sediment samples. We used a recently developed bioinformatics pipeline and two taxonomic assignment methods to resolve and assign amplicon sequence variants (ASVs) from Illumina amplicon data. We analysed the community composition recovered by both methods and tested the effects, on the levels of diversity detected by the metabarcoding method, of sieving samples prior to DNA extraction. 3. Metabarcoding of the mitochondrial marker cytochrome c oxidase I (COI) gene recovers the presence of more taxonomic groups than the morphological approach. We found that sieving samples results in lower alpha diversity detected and suggests a community composition that differs significantly from that suggested by un-sieved samples in our metabarcoding analysis. We found that whilst metabarcoding and morphological approaches detected similar numbers of species, they are unable to identify the same set of species across samples. 4. Synthesis and Applications We show that metabarcoding using the COI marker provides a more holistic, community-based, analysis of benthic invertebrate diversity than a traditional morphological approach. We also highlight current gaps in reference databases and bioinformatic pipelines for the identification of intertidal benthic invertebrates that need to be addressed before metabarcoding can replace traditional methods. Ultimately, with these limitations taken into consideration, resolving community-wide diversity patterns with metabarcoding could improve the management of non-protected marine habitats in the U.K.14-Jul-2020

opencc-zeroAug 2020View details →

dryad32/100

A national scale BioBlitz using citizen science and eDNA metabarcoding for monitoring coastal marine fish

Marine biodiversity is threatened by human activities. To understand the changes happening in aquatic ecosystems and to inform management, detailed, synoptic monitoring of biodiversity across large spatial extents is needed. Such monitoring is challenging due to the time, cost, and specialized skills that this typically requires. In an unprecedented study, we here combined citizen science with eDNA metabarcoding to map coastal fish biodiversity at a national scale. We engaged 360 citizen scientists to collect filtered sea water samples from 100 sites across Denmark over two seasons (1 pm on September 29th 2019 and May 10th 2020), and by sampling at nearly the exact same time across all 100 sites, we obtained an overview of fish biodiversity largely unaffected by temporal variation. This would have been logistically impossible for the involved scientists without the help of volunteer citizens. We obtained a high return rate of 94% of the samples, and a total richness of 52 fish species, representing approximately 80% of coastal Danish fish species and approximately 25% of all Danish marine fish species. We retrieved distribution patterns matching known occurrence for both invasive, endangered, and cryptic species, and detected seasonal variation in accordance with known phenology. Dissimilarity of eDNA community compositions increased with distance between sites. Importantly, comparing our eDNA data with National Fish Atlas data (the latter compiled from a century of observations) we found positive correlation between species richness values and a congruent patterns of community compositions. These findings support the use of eDNA-based citizen science to detect patterns in biodiversity, and our approach is readily scalable to other countries, or even regional and global scales. We argue that future large-scale biomonitoring will benefit from using citizen science combined with emerging eDNA technology, and that such an approach will be important for data-driven biodiversity management and conservation.

opencc-zeroFeb 2022View details →

dryad32/100

Data from: Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat

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publicMar 2019View details →

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Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record