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.
2,610
datasets available to search
ShareScore release 0.7.1
Dataset results
2,610 results for “TRACK”
U.S. household food waste tracking data in support of Li et al. 2023
These data were used to generate the results in the article “Household Food Waste Trending Upwards in the United States: Insights from a National Tracking Survey,” by Ran Li, Yiheng Shu, Kathryn E. Bender & Brian E. Roe, which has been accepted for publication in the Journal of the Agricultural and Applied Economics Association (doi – https://doi.org/10.1002/jaa2.59). The Stata code used to generate results is available from the authors upon request. U.S. residents who participate in consumer panels managed by a commercial vendor were invited by email or text message to participate in a two-part online survey during four waves of data collection: February and March of 2021 (Feb 21 wave, 425 initiated, 361 completed), July and August of 2021 (Jul 21 wave, 606 initiated, 419 completed), December of 2021 and January of 2022 (Dec 21 wave, 760 initiated, 610 completed), and February, March and April of 2022 (Feb 22 wave, 607 initiated, 587 completed), July, August and Septemper of 2022 (Jul 22 wave, 1817 initiated, 1067 completed). We are not able to determine if any respondents participated in multiple waves, i.e., if any of the observations are repeat participants. All participants provided informed consent and received compensation. Inclusion criteria included age 18 years or older and performance of at least half of the household food preparation. No data was collected during major holidays, i.e., the weeks of the Fourth of July (Independence Day), Christmas, or New Years. Recruitment quotas were implemented to ensure sufficient representation by geographical region, race, and age group. Post-hoc sample weights were constructed to reflect population characteristics on age, income and household size. The protocol was approved by the local Internal Review Board. The approach begins with participants completing an initial survey that ends with an announcement that a follow-up survey will arrive in about one week, and that for the next 7 days, participants should pay clo
Ground-truthing of satellite imagery to track harmful algal blooms in Pigeon Lake, Alberta, Canada 2017-2022
This data was collected to create a calibrated model that would enable the use of satellite imagery to track harmful algal blooms by using chlorophyll a estimates as a proxy for cyanobacteria in the lake. Samples from Pigeon Lake were collected on the same day that the Sentinel-2 satellite would pass over the lake. These samples were analyzed for different algal pigments and enumerated to genus level to ensure that the satellite imagery was of cyanobacteria rather than different algal groups. An algorithm was developed which we termed the three band index (TBI) that best matched with the cholorophyll a from the in situ samples. This model was used on satellite imagery from 2017-2022 of Pigeon Lake to get chlorophyll a estimates for every 20 x 20 pixel of each image of the lake. This pixel data was used to determine different bloom metrics like the intensity, the area (extent) and severity.
American alligator GPS tracking study from May 2008 to September 2010 on Sapelo Island, Georgia
We deployed GPS tracking units on seven adult American alligators (two females and five males), for periods ranging from 34 to 100 days from May 2008 to September 2010 on Sapelo Island, Georgia. GPS units were set to record the location of tracked alligators every 1.5 to 2 hours. GPS data were then downloaded and tracks analyzed using GIS software after recapture.
Data and code from "Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability" Kaiser et al. 2024 Ecology and Evolution
Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing ‘green’ season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a two-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons. These data were gathered as part of the Hubbard Brook Ecosystem Study (HB
Rodent declines track regional climate variability in North American drylands
Regional long-term monitoring can enhance the detection of biodiversity declines associated with climate change, improving future projections by reducing reliance on space-for-time substitution and increasing scalability. Rodents are diverse and important consumers in drylands, which cover ~45% of Earth’s land surface and face increasingly drier and more variable climates. Here, we analyzed abundance data for 22 rodent species across grassland, shrubland, ecotone, and woodland habitats in the southwestern USA. We captured two time series: 1995-2006 and 2004-2013 that coincide with phases of the Pacific Decadal Oscillation (PDO), which influences drought in southwestern North America. Regionally, rodent species diversity declined 20-35%, with greater losses during the later time period. Abundance also declined regionally, but only during 2004-2013, with losses of ~5% of animals captured. During the first time series (PDO wet phase), plant productivity outranked climate variables as the best regional predictor of rodent abundance for 70% of taxa, whereas during the second period (dry phase), climate best explained rodent abundance for 60% of taxa. Temporal dynamics in rodent diversity and abundance differed spatially among habitats and sites, with the largest declines in woodlands and shrublands of central New Mexico and Colorado. Both habitat type and phase of the PDO modulated which species were winners or losers under increasing drought and amplified interannual variability in drought. Fewer taxa were significant winners (18%) than losers (30%) under drought, but the identities of winners and losers differed among habitats for 70% of taxa. Our results suggest that the sensitivities of rodent species to climate contributed to regional declines in diversity and abundance during 1995 - 2013. Whether these changes portend future declines in drought-sensitive consumers in the southwestern USA will depend on the climate during the next major phase of the PDO.
SEV LTER: Tracking Vegetation Phenology Using PhenoCam Imagery at the Sevilleta National Wildlife Refuge, New Mexico, 2014-2024
As of 03/03/2024, the Sevilleta Long-Term Ecological Research Program is equipped with a total of 65 digital RGB cameras, or PhenoCams, across the Sevilleta National Wildlife Refuge. These cameras are installed on eddy covariance flux towers and at a number of precipitation manipulation experiments to track vegetation phenology and productivity across dryland ecotones. PhenoCams have been paired with eddy covariance flux tower data at the site since 2014, while some Mean-Variance Experiment PhenoCams were installed as recently as June 2023. For information on PhenoCam data processing and formatting, see Richardson et al., 2018, Scientific Data (https://doi.org/10.1038/sdata.2018.28), Seyednasrollah et al., 2019, Scientific Data (https://doi.org/10.1038/s41597-019-0229-9), and the PhenoCam Network web page (https://phenocam.nau.edu/webcam/). The PhenoCam Network uses imagery from digital cameras to track vegetation phenology and seasonal changes in vegetation activity in diverse ecosystems across North America and around the world. Imagery is uploaded to the PhenoCam server hosted at Northern Arizona University, where it is made publicly available in near-real time, every 30 minutes from sunrise to sunset, 365 days a year. The data are processed using simple image analysis tools to yield a measure of canopy greenness, from which phenological metrics are extracted, characterizing the start and end of the growing season. These transition dates have been shown to align well with on-the-ground observations at various research sites. Long-term PhenoCam data can be used to track the impact of climate variability and change on the rhythm of the seasons.
Multiple-object tracking as atool for parametrically modulating memory reactivation
Open the record for dataset details and reuse information.
Five-minute average cruise track and ship velocity of the Antarctic Circumnavigation Expedition (ACE) undertaken during the austral summer of 2016/2017.
<p><strong>Dataset abstract</strong></p> <p>The ship's cruise track, velocity, course over ground and heading at one-minute resolution for all five legs of the Antarctic Circumnavigation Expedition (ACE) are derived from a combination of:<br> - the latitude/longitude record of the Quality-checked, one-second cruise track for 21.12.2016 to 11.04.2017.<br> - the latitude/longitude record of the Uncorrected inertial navigation dataset (one-second resolution) for 27.11.2016 to 21.12.2016<br> - the latitude/longitude record of the raw meteorological data (30-second resolution) from 17.11.2016 to 27.11.2016<br> - where no latitude/longitude record at one-second resolution is available and the ship's velocity was above 2 meters per second, the three-second resolution record of the true and relative wind speed and direction, as well as the heading are used to re-calculate the ship's velocity under the assumption that the course of the ship equalled the heading.</p> <p>Basic filtering are applied to remove erroneous observations before the data are averaged to a one-minute resolution (DOI: 10.5281/zenodo.3752667).<br> The one-minute time series are averaged to five-minute resolution, whereby the vector averaging is used for the platform velocity and orientation.<br> For the latitude and longitude coordinates a simple average is calcualted, i.e., ignoring the curvature of the Earth.<br> Short stretches of missing coordinates are filled with linear interpolation between neighbouring observations.</p> <p><strong>Dataset contents</strong></p> <ul> <li>cruise-track-5min-legs0-4.csv, data file, comma-separated values</li> <li>data_file_header, metadata, text format</li> <li>README.txt, metadata, text format</li> <li>ace-cruise-track-5min-legs0-4-change-log.txt, metadata, text format</li> </ul> <p><strong>Change log</strong></p> <p><strong>v1.1</strong> - Added additional data coverage from 2016-11-17 - 2016-11-22 inclusive. Updated README.txt with information about data coverage. Added this change_log file.</p> <p><strong>v1.0</strong> - Initial release of averaged cruise track data set.</p> <p><strong>Dataset license</strong></p> <p>This five-minute averaged cruise track and velocity dataset is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0) whose full text can be found at https://creativecommons.org/licenses/by/4.0/</p>
Sex differences in visuomotor tracking
<p>This excel file contains individual data from two cohorts presented in our publication. </p> <p>Each excel sheet presents a separate portion of data (=>one sheet per figure)</p>
Weddell seal tracking data from the Weddell Sea (2011)
<p>This animation (.gif) comprises locations from 19 adult Weddell seals (<em>Leptonychotes weddellii</em>) instrumented in February 2011 with telemetry devices. These devices were Sea Mammal Research Unit Conductivity-Temperature-Depth Satellite Relay Data Loggers. These are animal-attached loggers that are manufactured and programmed by the Sea Mammal Research Unit Instrumentation Group at the University of St Andrews, Scotland. Ethical approval for this work was obtained from the University of St Andrews Animal Welfare and Ethics Committee, and from the corresponding committee at the British Antarctic Survey.</p> <p>This dataset is linked to the manuscript Photopoulou et al. 2020 "Sex-specific variation in the use of vertical habitat by a resident Antarctic top predator" Proceedings of the Royal Society B (http://dx.doi.org/10.1098/rspb.2020.1447) and a preprint on bioRxiv (https://doi.org/10.1101/2020.06.15.152009).</p> <p>The locations are the product of fitting a statistical model to the observed ARGOS location data, taking account of the error class. This animation does not show the originally observed locations. The model used was a continuous time state-space model implemented in the R package foieGras by Ian Jonsen and Toby Patterson (2019) foieGras: Fit Continuous-Time State-Space and Latent Variable Models for Filtering Argos Satellite (and Other) Telemetry Data and Estimating Movement Behaviour. R package version 0.4.01. <https://cran.r-project.org/package=foieGras></p> <p>The animation was created in R (R Core Team (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/) using the moveVis package by Jakob Schwalb-Willmann (2019). moveVis: Movement Data Visualization. R package version 0.10.2. https://CRAN.R-project.org/package=moveVis</p> <p>The background satellite image is generated by selecting the option [map_service = "mapbox"] in the moveVis function frames_spatial() that was used to generate the .gif file. This uses satellite maps from <a href="https://www.mapbox.com/maps/">https://www.mapbox.com/maps/</a></p> <p>Please note: the background satellite image is static and does not represent the sea ice conditions experienced by the seals in this dataset.</p>
More precise tracking of horizontal than vertical target motion with both the eyes and hand
<p>Those files contain individual data from a large cohort of participant (N=62). </p> <p>In the excel file (DATAmain), each sheet presents one set of variables (with individual value for each trial).</p> <p>This file contains information regarding eye and hand tracking performance (distance+lags), as well as smooth pursuit gains. </p> <p>The other files contain data that we used for the detailed analysis of saccades and lags, as well as the scripts that can be run with Perl. One script is for analysing the lag (Danion.pl) and the other one for analysing the saccades (saccades.pl). The other files (.txt and .dat) that were used for these analyses. Note that some library is needed (common_subroutines, draw_figure, and for the anova’s routines_that_use_R), meaning that you need to have R installed. </p> <pre>Regarding data acquisition we employed a program called Docometre that can be uploaded at the following address: http://139.124.68.1/buloup/index.php?selectedMenu=DOCoMETRe&lang=_fr When this program is installed, it needs to be run with BaselineTracking.dcm We also provide .BAS and .T91 files that correspond to the compiled version of each pattern Regarding visual stimuli, another program called ICE needs to be installed on a separate computer that receives information (target+cursor) from docometer, it can be uploaded at : https://trello.com/b/EtNCNrZH/icehttps://trello.com/b/EtNCNrZH/ice ICE needs to be run with Visuomotor.ice Visuomotor.icepro Visuomotor.txt and Visuomotor.icemat in the respective folder (icepro in Protocol folder, icemat and ice in Scenario Folder, and txt in Serie folder) Note that both Docometre and ICE need to be run with similar equipement as our (including Adwin Gold systems, Megatron joystick, video screen, graphic cards, and desktop eyelink providing analog signals to docometre). Adequate numbering of analogic channels needs also to be ensured. </pre>
Database - A Calculus of Tracking: Theory and Practice
<p>A manually curated sample (Top 100 Alexa domains only) of a OpenWPM database obtained from Princeton Web Census (https://webtransparency.cs.princeton.edu/webcensus/). The sample is used to instantiate the model for the paper "<a href="https://petsymposium.org/2021/files/papers/issue2/popets-2021-0027.pdf">A Calculus of Tracking: Theory and Practice</a>" to appear in PETS 2021.</p> <p>Accepted manuscript: https://petsymposium.org/2021/files/papers/issue2/popets-2021-0027.pdf</p> <p>GitHub page: https://github.com/giorgioditizio/calculus_of_tracking</p> <p> </p>
TokTrack: A Complete Token Provenance and Change Tracking Dataset for the English Wikipedia
<p><strong>Fixes in version 1.1 (= Zenodo's "version 2")</strong></p> <p>*In 20161101-revisions-part1-12-1728.csv, missing first data line is added.</p> <p>*In Current_content and Deleted_content files, some token values ('str' column) which contain regular quotes ('"') are fixed.</p> <p>*In Current_content and Deleted_content files, some wrong revision ID values for 'origin_rev_id', 'in' and 'out' columns are fixed.</p> <p> ------</p> <p><strong>This dataset contains every instance of all tokens (≈ words) ever written in undeleted, non-redirect English Wikipedia articles until October 2016, in total 13,545,349,787 instances. Each token is annotated with (i) the article revision it was originally created in, and (ii) lists with all the revisions in which the token was ever deleted and (potentially) re-added and re-deleted from its article, enabling a complete and straightforward tracking of its history.</strong></p> <p>This data would be exceedingly hard to create by an average potential user as it is (i) very expensive to compute and as (ii) accurately tracking the history of each token in revisioned documents is a non-trivial task. <br> Adapting a state-of-the-art algorithm, we have produced a dataset that allows for a range of analyses and metrics, already popular in research and going beyond, to be generated on complete-Wikipedia scale; ensuring quality and allowing researchers to forego expensive text-comparison computation, which so far has hindered scalable usage.</p> <p>This dataset, its creation process and use cases are described in a dedicated dataset paper of the same name, published at the ICWSM 2017 conference. In this paper, we show how this data enables, on token level, computation of provenance, measuring survival of content over time, very detailed conflict metrics, and fine-grained interactions of editors like partial reverts, re-additions and other metrics.</p> <p>Tokenization used: https://gist.github.com/faflo/3f5f30b1224c38b1836d63fa05d1ac94</p> <p>Toy example for how the token metadata is generated: <br> https://gist.github.com/faflo/8bd212e81e594676f8d002b175b79de8</p> <p><strong>Be sure to read the ReadMe.txt or - even more detailed - the supporting paper which is referenced under "related identifiers".</strong></p>
Moisture-Precipitation Couplings for Mesoscale Convective Systems in Tracking Data and Idealized Simulations
<p>Morphological properties, collocated synoptic conditions, and collocated rainfall for mesoscale convective systems in 1) the ISCCP Convective Tracking (CT) dataset with coincident data from the ERA-Interim (ERA-I) reanalysis and the Multi-Source Weighted-Ensemble Precipitation (MSWEP) product and 2) long-channel radiative-convective equilibrium (RCE) simulations in the System for Atmospheric Modeling (SAM).</p> <p><strong>ISCCP_tracking_colloc.tar.gz </strong>- NetCDF files by year from 2000 to 2004 inclusive including ISCCP-CT morphological properties of MCSs, a series of collocated synoptic variables from ERA-5 (including specific humidity, temperature, vertical velocity, and cloud condensate profiles), and collocated precipitation intensity and accumulation from MSWEP.</p> <p><strong>RCE_colloc_execution1.tar.gz</strong> - NetCDF files including RCE-SAM extent of MCSs (RCE_COL_cluster-sizes_*.nc), as well as collocated synoptic variables. Collocation of synoptic variables is performed for these files by extracting and averaging the variables over grid cells where the precipitation is greater than either its mean (RCE_COL_MEAN_*.nc) or its 99th percentile (RCE_COL_99_*.nc).</p> <p><strong>RCE_colloc_execution2.tar.gz</strong> - NetCDF files including RCE-SAM extent of MCSs (RCE_COL_cluster-sizes_*.nc), as well as collocated synoptic variables. Collocation of synoptic variables is performed for these files by taking either the mean (RCE_COL_MEAN_*.nc) or the 99th percentile (RCE_COL_99_*.nc) value over all grid cells within the MCS.<br><br>For the NetCDF files from RCE output, the numeric value in the file name is the corresponding sea surface temperature from 280 to 310 K.</p>
Research Data Alliance Interest Group Professionalising Data Stewardship Career Tracks Survey Dataset
<p>This is the final dataset resulting from the data steward Career Tracks survey that the Reseach Data Alliance (RDA) Interest Group Professionalising Data Stewardship carried out in 2022. Data stewards were defined as professionals who aim at guaranteeing that data is appropriately treated in all stages of the research cycle (i.e., design, collection, processing, analysis, preservation, data sharing and reuse); we invited responses from participants who either now or in the past carried out data stewardship functions, regardless of their job title. The survey asked respondents about their job titles, the organizational context in which they work(ed) including contract types and domains, their educational background, and how they perceive their professional future. </p><p>This dataset publication includes:</p><ol><li>Survey response data in CSV format. The file includes data from 241 respondents who consented to participate in the survey and share the data via a repsoitory, who indicated that they either currently work or have worked in the past in a data stewardship role, and who responded to at least one further question.</li><li>Thematic analysis of the qualitative questions Q11 and Q12 in PDF format.</li></ol>
Tracking Down Chimeric Assemblies In The TrackIt DNA Ladder Using Nanopore Sequencing
<h2>Dataset Description</h2><p>These files represent two different LSK114 sequencing runs on a TrackIt 1kb Plus DNA Ladder sample, and associated data analysis.</p><ul><li>July 20 2023 Flongle Run (191 Mb; 465k reads)<ul><li>pod5_files_2023-Jul-20_DAE_DNA_Ladder.tar.gz<br>- raw POD5 format files</li><li>called_2023-Jul-20_DAE_DNA_Ladder_duplex.bam<br>- duplex called reads, called using dorado v4.0 with the 2023-09-22 bacterial methylation model</li><li>sequence_QC_2023-Jul-20_DAE_DNA_Ladder.pdf<br>- sequence length / quality QC plots</li><li>LAST_2023-Jul-20_DAE_DNA_Ladder_reads_vs_reference.tar.gz<br>- Alignment summary statistics from LAST mapping of reads to their associated reference</li><li>lengths_summary_2023-Jul-20_DAE_DNA_Ladder.txt<br>- Length / QC summary statistics</li></ul></li><li>October 12 2023 P2 Solo Run (1.95 Gb, 1.11M reads)<ul><li>pod5_files_2023-Oct-12_DNA-Ladder-1kbplus_fail.tar.gz<br>- raw POD5 format files (all failed reads)</li><li>pod5_files_2023-Oct-12_DNA-Ladder-1kbplus_pass_000-059.tar.gz<br>- raw POD5 format files (passed reads, bundle #000-059)</li><li>pod5_files_2023-Oct-12_DNA-Ladder-1kbplus_pass_060-119.tar.gz<br>- raw POD5 format files (passed reads, bundle #060-119)</li><li>pod5_files_2023-Oct-12_DNA-Ladder-1kbplus_pass_120-179.tar.gz<br>- raw POD5 format files (passed reads, bundle #120-179)</li><li>pod5_files_2023-Oct-12_DNA-Ladder-1kbplus_pass_180-222.tar.gz<br>- raw POD5 format files (passed reads, bundle #180-222)</li><li>called_2023-Oct-12_DNA-Ladder-1kbplus_duplex.bam<br>- duplex called reads [October 12, 2023], called using dorado v4.0 with the 2023-09-22 bacterial methylation model</li><li>sequence_QC_2023-Oct-12_DNA-Ladder-1kbplus.pdf<br>- sequence length / quality QC plots</li><li>LAST_2023-Oct-12_DNA-Ladder-1kbplus_reads_vs_reference.tar.gz<br>- Alignment summary statistics from LAST mapping of reads to their associated reference</li><li>lengths_summary_2023-Oct-12_DNA-Ladder-1kbplus.txt<br>- Length / QC summary statistics</li><li>ladder_seqs.fa<br>- assembled DNA ladder sequences, based on simplex reads</li></ul></li></ul><h3>Methods</h3><h3>Sample preparation</h3><p>Preparation of DNA for sequencing was carried out following the ONT Ligation Sequencing DNA V14 (SQK-LSK114) protocol, with modifications to exclude DNA repair, and keeping the sample in the same 1.5ml tube to reduce sample loss.</p><h4>Tris-buffered Saline (TBS) buffer preparation</h4><ol><li>1M stock of NaCl was made by adding 2.922g of NaCl into a 50 ml Falcon tube, then made up to 50 ml with MilliPore water</li><li>A 50 mM TBS stock was created by adding 750 μl 1M NaCl solution to a 15 ml Falcon tube, then made up to 15 ml using Qiagen Elution Buffer (EB, i.e. 10 mM Tris-HCl at pH 8.0)</li><li>The pH was confirmed to be 7.9-8.1 using a pH indicator strip (e.g. MColorpHast 6.5 - 10.0; MER1095430001)</li></ol><h4>End prep</h4><ol><li>1 μg DNA ladder (i.e. 10 μl of 0.1 μg / μl DNA ladder) was transferred into a 1.5ml Eppendorf DNA LoBind tube</li><li>The volume was topped up to 43.5 μl with TBS (i.e. 33.5 μl TBS)</li><li>3.5 μl Ultra II End-prep Reaction Buffer and 3 μl Ultra II End-prep Enzyme Mix was added</li><li>After mixing by gentle pipetting, the mixture was incubated at RT for 5 minutes, then 65 \degrees for 5 minutes</li></ol><h4>Bead cleanup</h4><ol><li>The mixture was combined with 60 μl Ampure XP beads, and incubated on a rotator mixer at RT for 5 minutes</li><li>The tube was transferred to a magnetic rack [https://www.printables.com/model/532085-open-walled-magnetic-rack]</li><li>After the supernatant became clear and colourless, supernatant was pipetted off</li><li>The magnetic beads were washed twice with 150 μl of an 80% ethanol solution</li><li>The sample was dried briefly for 30s, then eluted in 60 μl TBS</li></ol><h4>Adapter ligation and final bead cleanup</h4><ol><li>To the sample tube was added 25 μl ONT Ligation buffer (LNB), 5μl NEBNext Quick T4 DNA Ligase (reduced from the protocol-suggested 10μl because that was all that was left in the tube), and 5μl ONT Ligation Adapter (LA)</li><li>The tube was mixed by gentle pipetting, spun down for 1-3s on a mini centrifuge, then incubated for 10 minutes at RT</li><li>The mixture was combined with 40 μl Ampure XP beads (100μl Ampure XP beads were used for the Flongle sample), and incubated on a rotator mixer at RT for 5 minutes</li><li>The tube was transferred to a magnetic rack [https://www.printables.com/model/532085-open-walled-magnetic-rack]</li><li>After the supernatant became clear and colourless, supernatant was pipetted off</li><li>The magnetic beads were washed twice with 250 μl of ONT Long Fragment Buffer (LFB) for the P2 Solo run, and 250μl ONT Short Fragment Buffer <br>(SFB) for the Flongle run</li><li>The sample was dried briefly for 30s, then eluted for 10 minutes at 37 \degrees in 15 μl ONT Elution buffer (EB)</li></ol><h4>Addition of sequencing library buffers</h4><ol><li>A flow cell was prepared by flushing with ONT Flow Cell Flush (FCF) mixed with ONT Flow Cell Tether (FCT). For the P2 Solo, I used 500 μl of a 1170μl FCF solution that had 30μl FCT added to it; for the Flongle I used 60μl of a 117μl FCF solution that had 3 μl FCT added to it</li><li>1 μl of the eluted library was quantified on a Quantus Fluorometer, and approximately 50 fmol (assuming 1kb average length) was transferred to a new 1.5μl tube</li><li>For the P2 Solo run, the volume was topped up to 32 μl TBS; for the Flongle run, the volume was topped up to 12 μl TBS</li><li>To the sample tube was added ONT Sequencing Buffer (SB; P2 Solo - 100μl; Flongle - 30μl) and ONT Library Beads (LIB; P2 Solo - 68μl; Flongle - 20μl)</li><li>The flow cell was re-flushed with additional FCF/FCT mixture (500 μl for the P2 Solo; 30 μl for the Flongle)</li><li>The sequencing library was then added to the flow cell (200 μl for the P2 Solo; 30 μl for the Flongle)</li><li>The prepared flow cell was left for 10 minutes to allow the library to settle before starting sequencing</li></ol><h4>DNA Sequencing and basecalling</h4><ol><li>Sequencing was carried out using MinKNOW v23.04.6, sequencing in fast mode at 400 bases per second with a 20bp minimum sequence length and <br>5 kHz sampling rate, with reads output as POD5 files</li><li>The Flongle flow cell was run for a full standard run length (24h), whereas the PromethION flow cell was run for 1.5 hours (after which the <br>counts of 15kb reads exceeded 200)</li><li>Sequenced reads were recalled in standard (simplex) mode using Dorado v0.4.0 and the 2023-09-22 bacterial methylation model [res_dna_r10.4.1_e8.2_400bps_sup@2023-09-22_bacterial-methylation]</li></ol><h3>Bioinformatics Analysis of Ladder Sequences </h3><h4>Sequence assembly</h4><p>Assembly process for bands that are 3k in length and greater (done on LFB-depleted P2 Solo sequences): </p><ol><li>Filter >q20 reads for a 100bp region around the target length (e.g. 4950-5050bp for the 5k band) [High quality reads were not sufficient for the 15kb band; all reads were needed]</li><li>Chop the reads up with a 1000bp overlap (e.g. 3000bp for the 5k band). This works around a Canu expectation that any read overlaps should be less than X% of the read.</li><li>Assemble the reads with Canu v2.2 [#REF], treating them as "pacbio" reads (for correction and homopolymer compression), with the GenomeSize parameter set to the expected band length (e.g. GenomeSize=5000).</li><li>Extract the first reported assembled contig.</li><li>Map the contig to the nanopore adapter sequences, and trim to exclude any matching sequence.</li></ol><p>[Canu has a default genome size and read length cutoff of 1kb, and performs poorly on sequences shorter than this] <br><br>Assembly process for bands under 3k in length (done on LFB-depleted P2 Solo sequences):</p><ol><li>Filter >q20 reads for a 100bp region around the target length (e.g. 4950-5050bp for the 5k band) [High quality reads were not in sufficient abundance for the 100bp band; all reads were needed]</li><li>Assemble using a<a href="https://gitlab.com/gringer/bioinfscripts/-/blob/master/fastx-kassembler.pl"> kmer-based de-bruijn assembler</a>, trimming off low-count kmers</li><li>Extract the first reported trimmed assembled chain</li><li>Map the assembled chain to the nanopore adapter sequences, and trim to exclude any matching sequence</li><li>Use web BLASTn [#REF] to help trim any additional trailing non-matching sequence</li></ol><h4>Mapping</h4><ol><li>Use a <a href="https://gitlab.com/gringer/bioinfscripts/-/blob/master/fastx-kmapper.pl">kmer-based lightweight mapper</a> to map reads to assembled bands</li><li>Created LAST mismatch matrix using `last-train` on the 5k reads together, using the full assembled ladder sequences as a reference:<br>last-train -Q 1 ladder_seqs.fa 5k_reads.fq.gz</li><li>Mapped all reads to the assembled ladder sequences (only the reference corresponding to the most likely band source), retaining (for each read) the mapping that had the longest combined proportion of read and reference sequence mapped:<br>lastal -p bacterial.mat -P 10 ladder_seqs.fa reads_2023-Oct-12_DNA-Ladder-1kbplus_called_all.fq.gz | \ <br> ~/scripts/maf2csv.pl | \ <br> awk -F ',' '{print $0","($8/100 * $13/100)}' | \ <br> sort -t ',' -k 16rg,16 | sort -t ',' -k 1,1 -u | sort -t ',' -k 1r,1 | \ <br> perl -pe 's/,[^,]*$/\n/' > LAST_reads_vs_ladder_longestMatch.csv.gz</li></ol>
Properties of identified ship tracks
<p>The ship track database of is used, which used "day microphysics" images comprised of a composite of visible, near and thermal infrared channels were used to manually locate likely positions of ship tracks. Identification was assisted by examining the CDNC, calculated from the MYD06 level 2 cloud retrieval products from Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite. The CDNC is calculated based on the adiabatic assumption, using the cloud optical depth and cloud effective radius from the MODIS MYD06 level 2 product.</p><p>Ship locations were sourced from their automatic identification system (AIS) data, allowing an observed ship track to be linked to the generating ship. Local meteorology was gathered from the European Centre for Medium-Range Weather Forecasts ERA5 reanalysis data, and ships mass emission rates were calculated using their specific fuel consumption and estimated drag. </p><p>Data labels:</p><ul><li>trackno: Ship track identifier (-)</li><li>sox: SO emission rate (kg s^-1)</li><li>cbh: Cloud base height (m)</li><li>blh: Boundary layer height (m)</li><li>cth: Cloud top height (m)</li><li>spd_res: Relative velocity between ship velocity and wind velocity (m s^-1)</li><li>nd_cln: Background cloud droplet number concentration (cm^-3)</li><li>nd_pol: Ship track cloud droplet number concentration (cm^-3)</li><li>cf_liq: Liquid cloud fraction (-)</li><li>lwp: Liquid water path (g m^-2)</li><li>t1000: Temperature at 1000 hPa (K)</li><li>LTS: Low tropospheric stability (K)</li><li>ctt: Cloud top temperature (K)</li><li>ctrc: Cloud top radiative cooling (W m^-2)</li><li>is_coupled: Flag for cloud coupling according to cloud base height indicator (cbh<1000 m)</li></ul>
Fusion of Underwater Camera and Multibeam Sonar for Diver Detection and Tracking
<div><strong>Context</strong></div> <div> </div> <div>This dataset is related to previously published public dataset "Sonar-to-RGB Image Translation for Diver Monitoring in Poor Visibility Environments". <a href="../records/7728089">https://zenodo.org/records/7728089</a></div> <div>It contains ZED-right camera and sonar images collected from Hemmoor Lake and DFKI Maritime Exploration Hall.</div> <div> </div> <div>Sensors: Low Frq (1.2MHz) Blueprint Oculus M1200d Sonar and ZED Right Camera</div> <div> </div> <div><strong>Content</strong></div> <div> </div> <div>The dataset is created for Diver Detection and Diver Tracking applications.</div> <div> </div> <div>For the Diver Detection part, the dataset is prepared to train, validate and test YOLOv7 model.</div> <div>7095 images are used for training data, and 3095 images are used for validation data. These sets are augmented from originally captured and sampled ZED camera images. Augmentation methods are not applied to the Test data, which contains 822 images. Train and validation contain images from both the DFKI pool and Hemmor Lake, while the test data is only collected from the lake.</div> <div> </div> <div>To distinguish between the original image and the augmented image, check the name coding. </div> <div>Naming of object detection images:</div> <div>original_image_name.jpg</div> <div>if augmented:</div> <div>original_image_name_<augmentation_number_of_the_same_image>.jpg</div> <div> </div> <div>Object Detection Label Format: </div> <div>YOLO [(class), ((x_min + (x_max - x_min)/2) / image_width), ((y_min + (y_max - y_min)/2) / image_height), ((x_max - x_min) / image_width), ((y_max - y_min) / image_height)]</div> <div> </div> <div>Class: "diver", represented by "0" in object detection labels.</div> <div> </div> <div>Resolution of Object Detection Camera Images: 640x640</div> <div>Resolution of Object Tracking Camera Images: 1280x720</div> <div>Resolution of Object Tracking Low Frequency Sonar: 932x514</div> <div> </div> <div>About the Object Tracking on Sonar, the sampled data is the part where diver moves around the table and the platform. </div> <div>There are 4 cases shared in the dataset, which contain a sonar stream, and corresponding ZED-right camera images. </div> <div>Totally, 1193 points represent the diver on sonar images for the diver tracking application.</div> <div> </div> <div>For the tracking, "tracking_sonar_coordinates_<number>.csv" contains x,y coordinates of a point where the diver is in the sonar image. </div> <div>And "image_sonar_<number>.csv" file contains the matching between sonar and camera images.</div> <div> </div> <div><strong>Acknowledgements</strong></div> <div> </div> <div>The data in this repository were collected as a joint effort between the German Center for Artificial Intelligence (DFKI), the German Federal Agency for technical Relief (THW), and Kraken Robotics GmbH. This work is part of the project DeeperSense that received funding from the European Commission. Program H2020-ICT-2020-2 ICT-47-2020 Project Number: 101016958.</div> <p> </p>
Feasibility of 3D Body Tracking from Monocular 2D Video Feeds in Musculoskeletal Telerehabilitation
<p>Musculoskeletal conditions affect millions of people globally, however, conventional treatments pose challenges concerning price, accessibility, and convenience. Many telerehabilitation solutions offer an engaging alternative but rely on complex hardware for body tracking. This work explores the feasibility of models for 3D Human Pose Estimation (HPE) from monocular 2D videos (MediaPipe Pose) in a physiotherapy context, by comparing its performance to ground truth measurements. MediaPipe Pose was investigated in eight exercises typically performed in musculoskeletal physiotherapy sessions, where the Range of Motion (ROM) of the human joints was the evaluated parameter. This model showed the best performance for shoulder abduction, shoulder press, elbow flexion, and squat exercises (MAPE ranging between 14.9% and 25.0%, Pearson’s coefficient ranging between 0.963 and 0.996, and cosine similarity ranging between 0.987 and 0.999). Some exercises (e.g. seated knee extension and shoulder flexion) posed challenges due to unusual poses, occlusions and depth ambiguities, possibly related to a lack of training data. This study demonstrates the potential of HPE from monocular 2D videos, as a markerless, affordable and accessible solution for musculoskeletal telerehabilitation approaches. Future work should focus on exploring variations of the 3D HPE models trained on physiotherapy-related datasets, such as the Fit3D dataset, and post-preprocessing techniques to enhance the model's performance.</p>
Eye tracking videos and raw data of breathing recognition attempts in simulated out-of-hospital cardiac arrest
<div> <div> <div> <p>This dataset comprises eye tracking videos and raw data documenting attempts to recognize breathing in simulated out-of-hospital cardiac arrest scenarios.</p> <p>The data were recorded using an Ergoneers Dikablis head-mounted eye tracker.</p> <p>Our analysis of this data resulted in the publication of two studies: Study 1, available at <a href="https://doi.org/10.1097/SIH.0000000000000617" target="_blank" rel="noopener">https://doi.org/10.1097/SIH.0000000000000617</a>, and Study 2, accessible at <a href="https://doi.org/10.25894/ijfae.2307" target="_blank" rel="noopener">https://doi.org/10.25894/ijfae.2307</a></p> <p> </p> <p>Version 2 is up-to-date.</p> <p>In Version 1:</p> <ul> <li>the doi for Study 2 was incorrect</li> <li>data for participant #51 of Study 1 were missing</li> </ul> </div> </div> </div>
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.