Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
101
datasets available to search
ShareScore release 0.9.0
Dataset results
101 results for “vessel data”
2d U-net models trained to segment human placental maternal/fetal blood volumes and blood vessels from syncrotron micro-CT data along with a sample data volume.
<p>This dataset contains a 512 x 512 x 512 pixel volume taken from an imaging dataset of human placental tissue collected at Diamond Light Source Manchester Imaging Branchline, I13-2 on visits MG23941 and MG22562 using in-line high-resolution synchrotron-sourced phase contrast micro-computed X-ray tomography. This data is saved in HDF5 format with a uint8 datatype. Alongside this are two 2d binary U-net models that have been trained to segment this data. One model segments the data into regions of maternal/fetal blood volume, the other segments the blood vessels. Both models were trained using the fastai python package, which utilises the pytorch library. These models were used to segment the data in our paper "A massively multi-scale approach to characterising tissue architecture by synchrotron micro-CT applied to the human placenta" which can be found at <a href="https://www.biorxiv.org/content/10.1101/2020.12.07.411462v1">https://www.biorxiv.org/content/10.1101/2020.12.07.411462v1</a>. The code used for training the U-net models and for predicting the segmentation of the data volume can be found at <a href="https://github.com/DiamondLightSource/placental-segmentation-2dunet">https://github.com/DiamondLightSource/placental-segmentation-2dunet</a> and is published at <a href="https://doi.org/10.5281/zenodo.4252562">https://doi.org/10.5281/zenodo.4252562</a> </p>
Validation data set for automatic blood vessel segmentation in colorectal cancer histology (IHC)
<p><strong>Content</strong></p> <p>This data set contains 100 histological image patches of 1000 * 1000 px size. The samples were immunostained for CD34 (3,3'-Diaminobenzidine, DAB [brown]) with hematoxylin (blue) counterstain.</p> <p>Furthermore, the data set contains a table of blood vessel counts in each image by three blinded observers as well as an automatic count with a method based on the following paper:</p> <p>Kather, Jakob Nikolas et al. "Continuous Representation Of Tumor Microvessel Density And Detection Of Angiogenic Hotspots In Histological Whole-Slide Images". <em>Oncotarget</em> 6.22 (2015): 19163-19176. http://dx.doi.org/10.18632/oncotarget.4383</p> <p><strong>Image format</strong></p> <p>All images are RGB, 0.50 µm per pixel, digitized with an Aperio ScanScope (Aperio/Leica biosystems), magnification 20x. Histological samples are fully anonymized images of formalin-fixed paraffin-embedded human colorectal adenocarcinomas (primary tumors and liver metastases) from our pathology archive (Institute of Pathology, University Medical Center Mannheim, Heidelberg University, Mannheim, Germany).</p> <p><strong>Ethics statement</strong></p> <p>All experiments were approved by the institutional ethics board (medical ethics board II, University Medical Center Mannheim, Heidelberg University, Germany; approval 2015-868R-MA). The institutional ethics board waived the need for informed consent for this retrospective analysis of anonymized samples. All experiments were carried out in accordance with the Declaration of Helsinki.</p> <p><strong>Contact</strong></p> <p>For questions, please contact:<br> Dr. Jakob Nikolas Kather<br> http://orcid.org/0000-0002-3730-5348<br> ResearcherID: D-4279-2015</p>
Observational data in the maiden voyage of the Sun Yat-sen University Research Vessel
<p>From 15 to 18 June 2022, the Sun Yat-sen University research vessel conducted its maiden voyage for scientific expedition in northern SCS. Radiosonde-equipped sounding balloons were launched up during the observation period to measure meteorological elements. </p> <p>This dataset encompasses a range of parameters, sequentially detailing Elapsed Time, Ascension Rate, Height Above Mean Sea Level, Atmospheric Pressure, Ambient Temperature, Relative Humidity, Dew Point Temperature, Wind Direction, and Wind Speed. During the observation period, the data obtained from the radiosonde measurements are as follows:</p>
Data from: Evaporation induced acoustic emissions in microfluidic vessels
<p>Fluid flow processes such as drainage and evaporation in porous media are crucial in geological and biological systems. The motion of the displacement front of a moving fluid through multi-phase interfaces is often associated with abrupt mechanical energy release, detectable as acoustic emissions. The exact origin of these pulses and their damping mechanisms are still subjects of debate. Here, we study the characteristics of such acoustic emissions during evaporation of water from artificial microfluidic vessels, inspired by the physiology of vascular water-transport in plants. From the extracted settling times of the recorded acoustic emissions, we identify three pulse types and attribute their origins to bubble formation, snap-off events and rapid pore invasion. We also show that the resonance frequencies between 10 and 70 kHz present in specific pulse types decrease with increasing vessel radius (ranging from 0.25 to 1.0 mm) and length (ranging from 2.5 to 10.0 mm). Our findings provide insight into evaporation-induced acoustic emissions from microfluidic systems, both natural and artificial, and their potential use in non-invasive inspection or vascular health monitoring.</p>
Data from: Evaporation induced acoustic emissions in microfluidic vessels
Open the record for dataset details and reuse information.
Data from: Vessel noise prior to pile driving at offshore windfarm sites deters harbour porpoises from potential injury zones
Open the record for dataset details and reuse information.
MarTREC Data Set for Report: Developing and Applying an Analysis Methodology to Identify Flow Generation Influences between Vessel and Truck Shipments
<p>Truck activity is logically connected to vessel activity at a port. In turn, vessel activity is also influenced by truck shipments. Although one might expect a direct and straightforward relation between these two types of shipments, that is rarely the case. For instance, many maritime containers carry consolidated cargos that have multiple and different final destinations. Also, different truck capacities, customs clearance and regulations play a critical role in determining the actual relation between these two types of shipments. This project aims at shedding light on the nuances of maritime and roadway flow relations by quantitatively analyzing the linkages between these two types of shipments.</p> <p>The study performed a statistical analysis to determine the probability distributions of vessel and truck activity, and then explore the correlation of each activity with the other. The analysis yielded coefficients that function as explanatory values for specific truck flows.</p> <p>The ultimate purpose of this study is to provide a clearer and quantitative understanding of the relationship between maritime and truck shipments, and by doing so, to provide tools to develop a system for managing trucks that maximizes efficiency for industry, while minimizing industry’s negative impacts on a region.</p> <p>For this purpose, the study selected the Port Freeport as a case study.</p>
Data from: Acoustically advertising male harbour seals in southeast Alaska do not make biologically relevant acoustic adjustments in the presence of vessel noise
Aquatically breeding harbour seal (Phoca vitulina) males use underwater vocalizations during the breeding season to establish underwater territories, defend territories against intruder males, and possibly to attract females. Vessel noise overlaps in frequency with these vocalizations and could negatively impact breeding success by limiting communication space. In this study we investigated whether harbour seals employed anti-masking strategies to maintain communication in the presence of vessel noise in Glacier Bay National Park and Preserve, Alaska. Harbour seals in this location did not sufficiently adjust source levels or acoustic parameters of vocalizations to compensate for acoustic masking. Instead, for every 1 dB increase in ambient noise, signal excess decreased by 0.84 dB, indicating a reduction in communication space when vessels passed. We suggest that harbour seals may already be acoustically advertising at or near a biologically maximal sound level, and therefore lack the ability to increase call amplitude to adjust to changes in their acoustic environment. This may have significant implications for this aquatically breeding pinniped, particularly for populations in high noise regions.
Data from: Recreational vessel networks reveal potential hot spots for marine pest introduction and spread
<p>Recreational vessels are an important pathway for spreading marine non-indigenous species (NIS) around coastal environments globally. However, most vessels are not tracked, limiting our ability to map their movements and identify locations at greater risk of NIS introductions. Using New Zealand as a case study, we quantified spread and risk patterns of recreational vessel movements, using a web-based survey allowing the more than 1,800 respondents to map significant trips with over 12,000 visits. These vessel routes were used to build a network model representing nationwide recreational vessel movements. Two proxies were used to quantify the risk of introduction of marine NIS: (i) incoming hull length and (ii) cumulative residency periods at sites. There was significant variation in the distances travelled, the destinations they visited, and the duration of their stays. New Zealand's recreational boating network contained 317 destinations with over 4,000 unique connections, concentrated within two distinct areas of the country. Network-based metrics and risk proxies quantified the relative importance of domestic locations as incursion or spreading hubs for NIS. This approach highlighted several areas that pose high relative biosecurity risk within the national network, but are underrepresented within current surveillance programmes. Synthesis and applications. Our study demonstrates how the movement dynamics of recreational vessels can be quantified at a regional scale to inform proactive management. The identification of spreading hubs and locations at particular risk of NIS introductions, enables managers to design risk-based and effective surveillance and monitoring programmes. Our network-based approach to determine the biosecurity implications posed by recreational vessels is transferable to other parts of the world. It enables managers to understand the distribution of risk within an area of interest (e.g., a jurisdiction) and develop optimised approaches for mitigating impact.</p>
X-Rays micro-tomography of 54 Egyptian predynastic ceramic vessels from the MAN (Musée d'Archéologie Nationale-Domaine national du château de Saint-Germain-en-Laye, France) made in the frame of the project TECHNOPREGYPT 2021/43/P/HS3/03262. STACK DATA
<p><span>54 complete pots and sherds from the collection of the <span><span>Musée d’Archéologie Nationale-Domaine national du château de Saint-Germain-en-Laye, France, were scanned with X-Rays microtomography (CT-Scan) to carry out the technological analysis of the samples. The aim was to be able to see the internal structure of the ceramic vessels to reconstruct the manufacturing process. </span></span></span></p> <p><span>The scans are part of the project </span><span>TECHNOPREGYPT</span><em><span> <span>Ceramic technology and the socio-political environment of Predynastic Egypt</span></span></em><span><span> </span></span><span><span>2021/43/P/HS3/03262 directed by dr Jade BAJEOT. </span></span></p> <p><a title="TECHNOPREGYPT website" href="https://technopregypt.iksio.pan.pl/index.php/about-the-project"><span><span>TECHNOPREGYPT website</span></span></a></p> <p> </p> <p><strong>Funding</strong></p> <p><span>This research was led at the Institute of Mediterranean and Oriental Cultures, Polish Academy of Sciences and was </span><span>co-funded by the Polish National Science Centre and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 945339.</span><strong><span> </span></strong><span>For the purpose of Open Access, the author has applied a CC-BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.</span></p>
Data from: The intraspecific relationship between wood density, vessel diameter and other traits across environmental gradients
<p>This data is about several traits measured on branches of 3 wide-niche breadth tree species--Embothrium coccineum (Proteaceae, Nothofagus antarctica (Nothofagaceae) and N. pumilio--growing across environmental gradients in southern Chile. The traits involve leaf, wood anatomy, including wood density, growth, carbon reserves and wood isotopes.</p>
Data for publication 'Recreational vessels without Automatic Identification System (AIS) dominate anthropogenic noise contributions to a shallow water soundscape' (Scientific Reports 2019)
<p>Data on vessel tracks and underwater noise levels presented in the publication Hermannsen, L., Mikkelsen, L., Tougaard, J., Beedholm, K., Johnson, M. and P. T. Madsen, "Recreational vessels without Automatic Identification System (AIS) dominate anthropogenic noise contributions to a shallow water soundscape", Scientific Reports 9:15477 (<a href="https://doi.org/10.1038/s41598-019-51222-9">https://doi.org/10.1038/s41598-019-51222-9</a>).</p>
Males miss and females forgo: auditory masking from vessel noise impairs foraging efficiency and success in killer whales - CALIBRATED MOVEMENT DATA AND VARIABLES SUPPORTING ANALYSES
<p><strong>Description of the data and file structure<br></strong>This record contains data from animal-borne biologging instruments (Dtags) temporarily affixed to fish-eating killer whales, supporting the analyses presented in the following article:</p> <p> Tennessen. J.B., Holt, M.M., Wright, B.M., Hanson, M.B., Emmons, C.K., Giles, D.A., Hogan, J.T., Thornton, S.J., Deecke, V.B. 2024. Males miss and females forgo: auditory masking from vessel noise impairs foraging efficiency and success in killer whales. <em>Global Change Biology</em>.<strong> </strong>In press.</p> <p>The data include the following: (1) calibrated movement data from analyzed Dtag deployments, and (2) a spreadsheet containing the variables included in the fully-saturated and final models listed in Table 2 in the article cited above. All methodological details necessary to contextualize analysis procedures are provided in the methods section of the article. The following data files are available under separate DOIs: 10.5281/zenodo.13333019 - all 2009 & 2010 audio data; 10.5281/zenodo.13328931 - all 2011 & 2014 audio data.</p> <p>These data are provided by NOAA Fisheries' Northwest Fisheries Science Center, and Fisheries and Oceans Canada, to support reproducibility of all statistical analyses presented in the article. Please cite your usage of our data. For inquiries about data use, or for general questions, please contact Dr. Jennifer B. Tennessen, at jtenness@uw.edu.</p> <p> </p> <p><strong>Description of the movement data files<br></strong>The movement files have been calibrated from the raw data and are ready to use. The files contain the .mat extension, and need to be opened using Matlab and the tagtools tool kit available at https://github.com/animaltags . Tutorials for working with the toolkit are available at animaltags.org . These files contain several vector and matrix variables. We define those used in our analyses below. For questions about how to work with these files, please contact Dr. Jennifer B. Tennessen, at jtenness@uw.edu.</p> <p>Aw: calibrated triaxial accelerometer data (converted from tag frame to whale frame)</p> <p>fs: sample rate (50 Hz)</p> <p>head: animal's circular heading (rotation about the dorsal-ventral axis, in radians)</p> <p>Mw: calibrated triaxial magnetometer data (converted from tag frame to whale frame)</p> <p>p: depth (in meters)</p> <p>pitch: animal's pitch (rotation about the left-right axis, in radians)</p> <p>roll: animal's roll (rotation about the anterior-posterior axis, in radians)</p> <p>tempr: temperature recorded on tag (in Celsius)</p> <p>TT: time cues for the start and end of every analyzed dive within a deployment. This matrix contains 6 columns:<br>-col 1: start cue (in sec)<br>-col 2: end cue (in sec)<br>-col 3: maximum depth of dive (m)<br>-col 4: time cue at max depth (in sec)<br>-col 5: mean depth (m)<br>-col 6: mean compression</p> <p> </p> <p><strong>Description of the analyzed variables<br></strong>The data are provided column-wise in a spreadsheet, whereby each column contains one of several variables used to build the corresponding models listed in Table 2 in the above article. Model details are provided in the above article, including the statistical packages needed to run the models. </p> <p><em>The following is a list of variable names (column headers) and their corresponding definitions:<br></em><strong>bzsounds:</strong> binary presence (1)/absence (0) of buzz bouts within a dive. Buzzing is defined as the occurrence of echolocation clicks with an inter-click interval < 11 ms<br><strong>code:</strong> categorical identifier of the numerical week of year in which the tag was deployed (e.g., week 33 of 2009 is different than week 33 of 2011)<br><strong>deployment:</strong> the event whereby a tag was affixed to an individual killer whale and data were collected via tag sensors; each deployment was assigned a unique deployment ID, consisting of the first letter of the Genus and species names (“oo” for Orcinus orca), followed by two digits corresponding to the year (“09” = 2009), followed by the Julian day of the year (e.g. “234”), followed by a letter indicating the deployment order of the day. NRKW deployments were assigned a through l, and SRKW deployments were assigned m through z (e.g. “a” = first deployment of the day for NRKW, “m” = first deployment of the day for SRKW)<br><strong>durwho: </strong>duration of a whole dive, in seconds. Dives were defined as all departures from the surface, to at least 1 m or deeper, followed by a return to within 0.5 m of the surface<br><strong>divenum: c</strong>hronological identifier for dive position within a deployment (e.g., for the 10<sup>th</sup> dive within a deployment, divenum = 10)<br><strong>kindet: </strong>binary presence (1)/absence (0) of a prey capture event within a dive. Prey capture was informed by the occurrence of stereotyped movement signatures in sensor data indicative of prey capture, following an established method validated with visual and acoustic confirmation of predation events. Prey capture is defined as the occurrence of three movement variables indicative of prey capture (peak jerk, roll and heading variance) each exceeding pre-determined thresholds (see Tennessen et al. 2019b in above article for details)<br><strong>maxdep:</strong> maximum depth of a dive, in meters<br><strong>NLmax: </strong>the maximum noise level received during a dive, measured as the root-mean-square sound pressure level (dB re 1 mPa) within one second bins over the 15-45 kHz frequency band<br><strong>population:</strong> population to which the tagged whale belongs (NRKW = Northern Resident killer whale; SRKW = Southern Resident killer whale)<br><strong>sex:</strong> sex of tagged whale (F = female, M = male, NA = unknown)<br><strong>sc:</strong> binary presence (1)/absence (0) of slow-click sounds within a dive. Slow-clicking is defined as the occurrence of echolocation clicks with an inter-click interval >100 ms<br><strong>tagID:</strong> identifier for the individual tag used for each deployment<br><strong>year:</strong> year of deployment</p>
Data from: Addressing controversies in the xylem embolism resistance – vessel diameter relationship
<ol> <li class="MsoNormal">Although xylem embolism is a key process during drought-induced tree mortality, its relationship to wood anatomy remains debated. While the functional link between bordered pits and embolism resistance is known, there is no direct, mechanistic explanation for the traditional assumption that wider vessels are more vulnerable than narrow ones.</li> <li class="MsoNormal">We used data from 20 temperate broad-leaved tree species to study the inter- and intraspecific relationship of water potential at 50% loss of conductivity (<em>P</em><sub>50</sub>) with hydraulically-weighted vessel diameter (<em>D</em><sub>h</sub>) and tested its link to pit membrane thickness (<em>T</em><sub>PM</sub>) and specific conductivity (<em>K</em><sub>s</sub>) on species level.</li> <li class="MsoNormal">Embolism-resistant species had thick pit membranes and narrow vessels. While <em>D</em><sub>h</sub> was weakly associated with <em>T</em><sub>PM</sub>, the <em>P</em><sub>50</sub> – <em>D</em><sub>h</sub> relationship remained highly significant after accounting for <em>T</em><sub>PM</sub>. The interspecific pattern between <em>P</em><sub>50</sub> and <em>D</em><sub>h</sub> was mirrored by a link between <em>P</em><sub>50</sub> and <em>K</em><sub>s</sub>, but there was no evidence for an intraspecific relationship.</li> <li class="MsoNormal">Our results provide robust evidence for an interspecific <em>P</em><sub>50</sub> – <em>D</em><sub>h</sub> relationship across our species. As a potential cause for the inconsistencies in published <em>P</em><sub>50</sub> – <em>D</em><sub>h</sub> relationships, our analysis suggests differences in the range of traits values covered, and the level of data aggregation (species, tree, or sample level) studied.</li> </ol>
Data from: Sampling from commercial vessel routes can capture marine biodiversity distributions effectively
<p>Collecting fine-scale occurrence data for marine species across large spatial scales is logistically challenging but is important to determine species distributions and for conservation planning. Inaccurate descriptions of species ranges could result in designating protected areas with inappropriate locations or boundaries. Optimising sampling strategies, therefore, is a priority for scaling up survey approaches using tools such as environmental DNA (eDNA) to capture species distributions. In a marine context, commercial vessels, such as ferries, could provide sampling platforms allowing access to under-sampled areas and repeatable sampling over time to track community changes. However, sample collection from commercial vessels could be biased and may not represent biological and environmental variability. Here, we evaluate whether sampling along Mediterranean ferry routes can yield unbiased biodiversity survey outcomes, based on perfect knowledge from a stacked species distribution model (SSDM) of marine megafauna from online data repositories. Simulations to allocate sampling point locations were carried out representing different sampling strategies (random vs regular), frames (ferry routes vs unconstrained) and number of sampling points. SSDMs were remade from different sampling simulations and compared to the 'perfect knowledge' SSDM to quantify the bias associated with different sampling strategies. Ferry routes detected more species and were able to recover known patterns in species richness at smaller sample sizes better than unconstrained sampling points. However, to minimise potential bias, ferry routes should be chosen to cover the variability in species composition and its environmental predictors in the SSDMs. The workflow presented here can be used to design effective sampling strategies using commercial vessel routes globally, including for eDNA analyses. This approach has potential to provide a cost-effective method to access remote oceanic areas on a regular basis and can recover meaningful data on spatiotemporal biodiversity patterns.</p>
Data from: Monitoring temporal and spatial trends of illegal and legal fishing in Canada's marine conservation areas using vessel tracking datasets
<p>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.</p>
Data for: Small reductions in cargo vessel speed dramatically reduce noise impacts to marine mammals
<p><span>Global reductions in the underwater radiated noise levels from cargo vessels are needed to reduce increasing cumulative impacts to marine wildlife. We use a vessel exposure simulation model to examine how reducing vessel source levels through slowdowns and technological modifications can lessen impacts on marine mammals. We show that the area exposed to ship noise reduces dramatically with moderate source level reductions that can be readily achieved with small reductions in speed. Moreover, slowdowns reduce all impacts to marine mammals despite the longer time that a slower vessel takes to pass an animal. We conclude that cumulative noise impacts from the global fleet can be reduced immediately by slowdowns. This solution requires no modification to ships and is scalable – from local speed reductions in sensitive areas to ocean basins. Speed reductions can be supplemented by routing vessels away from critical habitats and by technological modifications to reduce vessel noise.</span></p>
Data from: Divergence of vessel diameter explains interspecific variation in hydraulic safety to salinity in the Sundarbans mangrove ecosystem
Open the record for dataset details and reuse information.
Data from: Sampling from commercial vessel routes can capture marine biodiversity distributions effectively
Open the record for dataset details and reuse information.
Data from: Climate change and pathways of vessel traffic create marine protected area networks of invasion
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.
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.
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.
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.