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408 results for “data repositories”
EPSRC HEED Data Repository: Footfall Monitoring System
<p>The dataset deposited here was prepared under the EPSRC-funded <a href="http://heed-refugee.coventry.ac.uk/">Humanitarian Engineering and Energy for Displacement</a> research project (EP/P029531/1). The project aimed to understand energy needs of displaced communities, create an evidence base on the usage of different energy interventions and provide recommendations for improved design of future energy interventions to better meet the needs of people. </p> <p>As part of the project, we deployed a Footfall Monitoring System in the Uttargaya settlement in Nepal. Footfall monitors are designed to measure the step count of passers-by with the aim to: Evaluate the level of activity in an area by measuring footfall count and Evaluate the effect of streetlights on the level of activity.</p> <p>For the purpose of this study, the 7 footfall monitors are deployed beside 7 streetlights. The footfall monitors were deployed prior to commissioning of streetlights to gather baseline data and evaluate the impact of streetlights on the footfall count. The key constituents of footfall monitors are: Raspberry Pi 3B and Case; PiFace Real Time Clock and CAM008 70º night vision camera. The total cost of a monitor is £92.88. The Raspberry Pi is the central unit of the system that runs a program to sense the footfall count as measured by the IR sensor. The IR sensor counts footfall by tracking the number of times a horizontal beam of light is “broken” when a person crosses a threshold. If new data is recorded by the sensor, the updated footfall count along with the direction of movement and the current time (measured from PiFace RTC) is stored onto an SD card. A packet containing the updated values is also transmitted to the heed-data server hosted at Coventry University.</p> <p>Post Deployment Challenges:</p> <ul> <li><strong>Damage to footfall</strong>: In April 2019, footfall monitor 7 was damaged due to a gust of storm and heavy rains in the camp. This monitor was replaced in May 2019.</li> <li><strong>Power outages:</strong> These are common in the camp. Data is lost during this time as the devices have no access to power.</li> <li><strong>Internet connectivity: </strong>The availability and reliability of Wi-Fi continue to be an issue for the transmission of data to heed-data server.</li> </ul>
Data quality assurance at research data repositories: Survey data
<p>This dataset documents findings form a survey on the status quo of data quality assurance practices at research data repositories.</p> <p>The personalized online survey was conducted among repositories indexed in re3data in 2021. It covered the scope of the repository, types of data quality assessment, quality criteria, responsibilities, details of the review process, and data quality information, and yielded 332 complete responses.</p> <p>The dataset comprises a documentation file, the data file, a codebook, and the survey instrument.</p> <p>The <strong>documentation file</strong> (documentation.pdf) outlines details of the survey design and administration, survey response, and data processing. The <strong>data file</strong> (01_survey_data.csv) contains all 332 complete responses to 19 survey questions, fully anonymized. The <strong>codebook</strong> (02_codebook.csv) describes the variables, and the <strong>survey instrument</strong> (03_survey_instrument.pdf) comprises the questionnaire that was distributed to survey participants.</p>
Data from calculated radial neutron flux distributions in a KBS-3 type geological repository
<p>Data from calculations of radial distribution of neutron flux per emitted neutron from rods of spent nuclear fuel in a KBS-3 type geological repository. Reference (<em>Jansson, 2022</em>) contain a summary of the calculations and a description of the structure of this data.</p> <p>This data was computed on resources provided by Swedish National Infrastructure for Computing (SNIC) at Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), National Supercomputer Centre at Linköping University (NSC) and the SNIC Cloud, partially funded by the Swedish Research Council through grant agreement no. 2018-05973, under projects SNIC 2021/5-299 and SNIC 2021/18-12.</p>
Raw Data for Mapping Repositories and their Institutional Open Science Policies in Asia
<p>Persistent Identifiers (PIDs), particularly Digital Object Identifiers (DOIs), are crucial for establishing a robust and globally accessible research infrastructure. In Asia, a diverse array of research outputs and resources are produced and published in repositories. However, a significant number of these repositories, and outputs remain undiscoverable in global registries and aggregators. <br><br>These three datasets provides comprehensive information on the adoption of repositories, Open Access mandates, and DOIs adoption in Asian countries. It includes detailed records from different registry sources and repository platforms.<br><br>You can read the full report titled 'Mapping Repositories and their Institutional Open Science Policies in Asia' at <a href="https://doi.org/10.5281/zenodo.12566244">https://doi.org/10.5281/zenodo.12566244</a></p>
Data Repository: Land surface modelling activities at Weierbach catchment.
<p>The data in this repository comes from the modelling activities with the Community Land Model version 5.0 (CLM5) carried out at the Weierbach catchment, Luxembourg. The repository contains:</p> <ol> <li>A list of matric potentials of <em>Fagus sylvatica </em>at which it experiences a specific loss of conductivity (i.e., 12%, 50%, 88%) obtained from published data [File: additional_PHT_Fagus_sylvatica_Europe.csv].</li> <li>The hourly atmospheric forcing used during the simulations with CLM 5.0 in a NetCDF format [File: atmospheric_forcing.zip].</li> <li>All model results per experiment [model_results.zip].</li> <li>The R scripts for processing the model results for obtaining the information required for each figure [Files: manuscript_figure_#.R].</li> <li>A daily summary of the tree water deficit calculated per PFT, individual tree species, and the whole ecosystem [File: twd.csv].</li> <li>A daily summary of tree transpiration scaled at the catchment level per PFT, individual tree species, and the whole ecosystem [File: et_mm_wei.csv]. This daily summary is based on the hourly data available on: Klaus, J., Fabiani, G., Schoppach, R., Chun, K. P., Iffly, J. F., Penna, D., & Juilleret, J. (2024). Detailed sap flow monitoring data at Weierbach catchment, Luxembourg (Version v01) [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.11381618" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11381618</a></li> </ol>
Listing of data repositories that embed schema.org metadata in dataset landing pages
<p>Machine-readable metadata available from landing pages for datasets facilitate data citation by enabling easy integration with reference managers and other tools used in a data citation workflow. Embedding these metadata using the schema.org standard with the JSON-LD is emerging as the community standard. This dataset is a listing of data repositories that have implemented this approach or are in the progress of doing so.</p> <p>This is the first version of this dataset and was generated via community consultation. We expect to update this dataset, as an increasing number of data repositories adopt this approach, and we hope to see this information added to registries of data repositories such as re3data and FAIRsharing.</p> <p>In addition to the listing of data repositories we provide information of the schema.org properties supported by these data repositories, focussing on the required and recommended properties from the "Data Citation Roadmap for Scholarly Data Repositories".</p>
Github commit data for the article "Beyond Zipf's law: Exploring the discrete generalized beta distribution in open-source repositories"
<p><span>This dataframe corresponds to the data used in the Nowak's et al. 2024 article "Beyond Zipf’s law: Exploring the discrete generalized beta distribution in open-source repositories" (see reference below).</span></p> <p><span>It consists of the distirbutions of number of commits per user across a number of GitHub repositories. <br><br>There are three columns:</span></p> <ul> <li><span>repository: the repository name</span></li> <li><span># of commits: the number of commits of a given individual</span></li> <li><span>rank: the user rank in the repository (by decreasing number of commits)<br><br></span></li> </ul> <p><strong><span>Reference:</span></strong></p> <p><span>Nowak, P., Santolini, M., Singh, C., Siudem, G., & Tupikina, L. (2024). Beyond Zipf’s law: Exploring the discrete generalized beta distribution in open-source repositories. <em>Physica A: Statistical Mechanics and Its Applications</em>, <em>649</em>, 129927. <a href="https://doi.org/10.1016/j.physa.2024.129927">https://doi.org/10.1016/j.physa.2024.129927</a></span></p>
Raw Data for Mapping Repositories and their Institutional Open Science Policies in the Middle East and North Africa (MENA)
<div> <p>Persistent Identifiers (PIDs), particularly Digital Object Identifiers (DOIs), are crucial for establishing a robust and globally accessible research infrastructure. In the Middle East and North Africa (MENA) region, a diverse array of research outputs and resources are produced and published in repositories. However, a significant number of these repositories, and outputs remain undiscoverable in global registries and aggregators. <br><br>These three datasets provides comprehensive information on the adoption of repositories, Open Access mandates, and DOIs adoption in MENA countries. It includes detailed records from different registry sources and repository platforms.<br><br>You can read the full report titled 'Mapping Repositories and their Institutional Open Science Policies in MENA' at <a href="https://doi.org/10.5281/zenodo.11370031">https://doi.org/10.5281/zenodo.11370031</a></p> </div>
A2.2a Digital repositories data citation practices. Supplementary material
<p>Data to complement the quantitative analysis of data citation practices in digital repositories based on metadata records from the re3data.org repositories registry.</p> <p>Data was retrieved using re3data.org API on 23-02-2023 and 06-03-2023 and processed using the OpenRefine software.</p> <p>Part of "A FAIR-enabling citation model for Cultural Heritage Objects" project activities.</p>
Coronavirus COVID-19 (2019-nCoV) Data Repository for Africa
<p>The purpose of this repository is to collate data on the ongoing coronavirus pandemic in Africa. Our goal is to record detailed information on each reported case in every African country. We want to build a line list – a table summarizing information about people who are infected, dead, or recovered. The table for each African country would include demographic, location, and symptom (where available) information for each reported case. The data will be obtained from official sources (e.g., WHO, departments of health, CDC etc.) and unofficial sources (e.g., news). Such a dataset has many uses, including studying the spread of COVID-19 across Africa and assessing similarities and differences to what’s being observed in other regions of the world.</p> <p>See the repo here <a href="https://github.com/dsfsi/covid19africa">https://github.com/dsfsi/covid19africa</a></p>
EPSRC HEED Data Repository: Stove Use Monitoring System
<p>The dataset deposited here was prepared under the EPSRC-funded <a href="http://heed-refugee.coventry.ac.uk/">Humanitarian Engineering and Energy for Displacement</a> research project (EP/P029531/1). The project aimed to understand energy needs of displaced communities, create an evidence base on the usage of different energy interventions and provide recommendations for improved design of future energy interventions to better meet the needs of people.</p> <p>As part of the project, we deployed Stove Use Monitoring Systems (SUM) on clay cook stoves in Kigeme camp, Rwanda. The aim was to (a) measure and evaluate temperature profiles within stove enclosure and on the surface of stoves (b) evaluate frequency and duration of stove use. The SUM consisted of 2 sensors - a thermocouple (to measure temperature within the stove) and a Si7021 sensor (to measure temperature and humidity outside the stove), connected to an Arduino MKR GSM 1400 board. The data measured by the sensors was stored only if the change in values exceeded a set threshold for either of the readings. The SUM was powered by a re-chargeable Li-Ion battery of 3.7V and a rating of 7.59Wh.</p> <p>The study was conducted in 2 phases. In phase 1 (02 July 2019 to 30 September 2019), data was collected from 15 SUM and stored locally on SD card as well as communicated to a remote server via GSM. The time of data collection was recorded using GSM functionality. However, several GSM and MQTT failures were noted leading to loss of timestamp values as well as shorter battery lifetime due to re-transmission tries. In phase 2 (02 October 2019 to 17 October 2019), data was collected from 9 SUM and only stored locally on SD cards. The time of data collection was recorded using an external RTC clock connected to the Arduino board. The data from both phases of study is deposited here along with the metadata.</p>
EPSRC HEED Data Repository: Lantern Monitoring System
<p>The dataset deposited here was prepared under the EPSRC-funded <a href="http://heed-refugee.coventry.ac.uk/">Humanitarian Engineering and Energy for Displacement</a> research project (EP/P029531/1). The project aimed to understand energy needs of displaced communities, create an evidence base on the usage of different energy interventions and provide recommendations for improved design of future energy interventions to better meet the needs of people.</p> <p>As part of the project, we deployed Lantern Monitoring Systems in Nyabiheke camp, Rwanda. The aim was to (a) evaluate lantern usage pattern – static or mobile (b) evaluate lantern charge and discharge pattern to understand consumption behaviour. The mobile lantern monitors comprise of a D.light S30 solar lantern fitted with an Arduino-based monitoring device. The most integral part of the device is the Arduino MKR GSM 1400 board connected to an ADXL345 inertial motion unit sensor. The ADXL is used to generate activity and freefall interrupts based on acceleration readings when the lantern is in use. These interrupts are, in turn, processed to calculate the step count of the user. Additionally, the voltage of lantern battery is measured using an in-house designed voltage monitor to evaluate the discharging and charging patterns. The updated values of step count, rate of change of steps and device and lantern battery voltage are stored only if a significant change in the step count is detected. The device is packaged within the lantern casing and powered through a re-chargeable Li-Ion battery of 3.7V and a rating of 7.59Wh.</p> <p>The study was conducted in 2 phases. In phase 1 (03 July 2019 to 30 September 2019), data was collected from 60 lanterns and stored locally on SD card as well as communicated to a remote server via GSM. The time of data collection was recorded using GSM functionality. However, several GSM and MQTT failures were noted leading to loss of timestamp values as well as shorter battery lifetime due to re-transmission tries. Moreover, several incidents of theft and device failures were reported leading to loss of data. In phase 2 (09 October 2019 to 18 December 2019), the design of lantern monitors was modified to fix these issues. The data was collected from 54 lanterns data and only stored locally on SD cards. The time of data collection was recorded using an external RTC clock connected to the Arduino board and internal watchdog timer was used to reset the device in case of failures. While certain failures persisted, the data yield was considerably higher than phase 1 of the study. The data from both phases of study is deposited here along with the metadata.</p>
Repository of data supporting the thesis "Poly-algorithmic Techniques in Real Quantifier Elimination"
<p>Dataset of various files (as a .zip) supporting the PhD thesis "Poly-algorithmic Techniques in Real Quantifier Elimination" by Zak Tonks, University of Bath. The PhD thesis is in the area of Quantifier Elimination over the Reals (QE) in Computer Algebra. The PhD thesis concerns implementation of algorithms in Quantifier Elimination, which largely culminates in the package QuantifierElimination for the Computer Algebra software Maple. Much of this repository is output of the benchmarking of this package against various other packes in Maple and otherwise. Otherwise there are some auxiliary tools and files to assist with working with QE in Maple, converting between various formats, and understanding case studies and the package QuantifierElimination via software demoes as Maple worksheets.</p> <p>An overview of the contents of this repository (as a .zip file, which contains subdirectories described in the README):</p> <ul> <li>The example databases contributed from the project, as files that can be read into Maple defining tables of examples, and associated functions to build or examine various examples,</li> <li>A pdf file providing the references for all examples from the example databases, and typesetting of the examples as associated QE problems,</li> <li>The benchmarking data produced from the benchmarking of the project as csv (comma separated value) files, and the Excel workbooks (xlsx files) processing said data into survival plots for the thesis,</li> <li>Copies of the survival plots themselves as .png files,</li> <li>The bash and Maple scripts used to generate the raw benchmarking data, that can be reused, including documentation how to do so in the associated README,</li> <li>Other auxiliary tools allowing for conversion of QE formulae between formats (such as that of SyNRAC, RegularChains, QuantifierElimination (amongst packages in Maple), and QEPCAD B.</li> <li>Maple worksheets and the associated exported pdf files used in software demos at conferences to demonstrate features of QuantifierElimination.</li> <li>Some pdf files demonstrating early case studies on Lazard curtains generated from an early development build of QuantifierElimination.</li> </ul> <p>Lastly, there is a README with more detail on the files of the repository further. To emulate the benchmarking of the thesis, an understanding of bash and potentially Maple is assumed, but the raw data from the project is provided here. Before QuantifierElimination's official release, the source code and/or Maple package as an .mla file is available for interested parties upon request to the author Zak Tonks (<a href="mailto:zak.p.tonks@bath.edu">zak.p.tonks@bath.edu</a>). Any other queries about this data or associated work should be directed to this email address. The author's PhD supervisor's email address is <a href="mailto:J.H.Davenport@bath.ac.uk">J.H.Davenport@bath.ac.uk</a>.</p>
EPSRC HEED Data Repository: Surveys
<p>The HEED project aims at understanding energy needs of refugees and displaced populations to improve access to clean energy. The focus of HEED is on the lived experiences of refugees living for protracted periods of time in three refugee camps in Rwanda (Nyabiheke, Gihembe and Kigeme) and internally displaced persons (IDPs) forced to leave their homes as a result of the 2015 earthquake in Nepal. As part of the project, an energy assessment survey of households in both countries was undertaken using quantitative and qualitative research methods with households living in different parts of the camps/settlements, entrepreneurs running small businesses, and those responsible for community facilities, such as schools and health clinics. In the first phase, a questionnaire-based survey targeting displaced populations was conducted with households living in three refugee camps in Rwanda and four displaced sites in Nepal (see tables 2.1 and 2.2 respectively). The second phase of the field research involved a series of interviews and focus group discussions with various stakeholders in Nepal and Rwanda. The surveys were designed and delivered between March and April 2018 by the project partner, Practical Action. In both countries, the enumerators for the survey received a two-day training on research methods, data collection and ethics. </p> <p>With regards to the household survey, the sample size was derived using Cochran’s formula as described by Bartlett et. al. in Organizational Research: Determining Appropriate Sample Size in Survey Research. A minimum sample size of 119 households was derived by applying a margin of error of 0.03 and an alpha of 0.5. A breakdown of the focal group and specific sites where the surveys were delivered in Rwanda and Nepal is shown in tables 2.1 and 2.2 respectively. In Rwanda, a total of 814 surveys including 622 households, 155 enterprises and 37 community facilities from across three sites were conducted. The sample distribution across camp shows 211 for Gihembe, 202 for Kigeme and 209 for Nyabiheke. In Gihembe more than half of the respondents (118, 55.9%) sampled were females with the remaining 93 (44.1%) being males. This is in contrast with Kigeme where almost equal numbers of both male (100, 49.5%) and females (102, 50.5%) were sampled. In Nyabiheke the sample covered more females (123, 58.9%) than males (86, 41.1%). In Nepal, the sample covered 181 households, 18 enterprises and 3 community facilities (see table 2.2). The household sample in Nepal covered more males (126, 69.6%) than females (55, 30.4%). </p> <p><strong>Folder Structure:</strong><br> <strong>Surveys:</strong></p> <p>Gihembe Community Facility Survey – Gihembe_CF.csv<br> Gihembe Enterprise Survey – Gihembe_EN.csv<br> Gihembe Household Survey – Gihembe_HH.csv</p> <p>Kigeme Community Facility Survey – Kigeme_CF.csv<br> Kigeme Enterprise Survey – Kigeme_EN.csv<br> Kigeme Household Survey – Kigeme_HH.csv</p> <p>Nepal Community Facility Survey – Nepal_CF.csv<br> Nepal Enterprise Survey – Nepal_EN.csv<br> Nepal Household Survey – Nepal_HH.csv</p> <p>Nyabiheke Community Facility Survey - Nyabiheke_CF.csv<br> Nyabiheke Enterprise Survey – Nyabiheke_EN.csv<br> Nyabiheke Household Survey – Nyabiheke_HH.csv</p> <p><strong>Location Maps</strong>:</p> <p>Gihembe Community Facility Survey Map – CF_GIS_gihembe.csv<br> Gihembe Enterprise Survey Map – EN_GIS_gihembe.csv<br> Gihembe Household Survey Map – HH_GIS_gihembe.csv</p> <p>Kigeme Community Facility Survey Map – CF_GIS_kigeme.csv<br> Kigeme Enterprise Survey Map – EN_GIS_kigeme.csv<br> Kigeme Household Survey Map – HH_GIS_kigeme.csv</p> <p>Nepal Community Facility Survey Map – CF_GIS_nepal.csv<br> Nepal Enterprise Survey Map – EN_GIS_nepal.csv<br> Nepal Household Survey Map – HH_GIS_nepal.csv</p> <p>Nyabiheke Community Facility Survey Map - CF_GIS_nyabiheke.csv<br> Nyabiheke Enterprise Survey Map – EN_GIS_nyabiheke.csv<br> Nyabiheke Household Survey Map – HH_GIS_nyabiheke.csv</p> <p>The following information was gathered from each of the surveys:</p> <ul> <li>Households: The datasets contain information about household demographics, access to and use of electricity and lighting technologies, access to and use of cooking technologies and fuels, self-reported needs and priorities by the household, and ownership of energy products. Several key areas, such as solar lighting products and issues around fuel usage, are covered in more detail. </li> <li>Enterprises: The datasets contain information about the enterprise, their electrical and non-electrical lighting needs and supply, the usage of energy for ICT and entertainment, motive power, heating, and cooling applications, and their ownership of electrical appliances. </li> <li>Community facility: The datasets contain information about the community facility or institution, their electrical and non-electrical lighting needs and supply, the usage of energy for ICT and entertainment, motive power, heating, and cooling applications, and their ownership of electrical appliances. Community facilities offered healthcare services were presented additional questions about specific medical devices. </li> </ul> <p>The survey results together with other methodological tools including field visits, workshops - ‘Design for Displacement (D4D)’ and ‘Energy for End-Users’ (E4E) workshops have provided relevant data and contextual knowledge to inform the design of the various interventions associated with the HEED. The data sets and results have been compiled, organised and uploaded in the data portal for use by researchers, students and all both within and outside of the project consortium, during and beyond the project lifetime.</p>
Research Data of the 2014 Census of Open Access Repositories in Germany, Austria and Switzerland
<p>The "2014 Census of Open Access Repositories in Germany, Austria and Switzerland” (2014 Census) is a study on the green open access landscape conducted in the course of a project seminar at the Berlin School of Library and Information Science (BSLIS) at Humboldt-Universität zu Berlin. The 2014 Census not only succeeds the "2012 Census of Open Access Repositories in Germany"[1] but enhances it by adding an online survey to the qualitative analysis of the open access repository websites and the automatic validation of its metadata. Like in 2012 the 2014 Census gives insights into the development of open access repositories and current trends in repository design being of substantial use to open access repository operators.</p> <p>This 2014 Census data set represents the data collected in three different ways:</p> <ul> <li>qualitative analysis of the open access repository websites</li> <li>automatic validation of the metadata via OAI-PMH using the DINI-Validator [2] </li> <li>online survey of repository operators</li> </ul> <p>As in 2012 [3] the data set is provided in XLSX as well as in CSV format. The columns represent the criteria and the rows represent the analyzed open access repositories. In the XLSX file the header row gives the definition of each criterion in English and German. In the CSV "content" file the header row is in English short terms. The respective English and German definition can be found in the CSV "readme" file.</p> <p> </p> <p>[1] Vierkant, P. (2013). 2012 Census of Open Access Repositories in Germany: Turning Perceived Knowledge Into Sound Understanding. <em>D-Lib Magazine</em>, 19. http://dx.doi.org/10.1045/november2013-vierkant </p> <p>[2] http://oanet.cms.hu-berlin.de/validator/pages/validation_dini.xhtml</p> <p>[3] Vierkant, Paul; Voigt, Michaela; Dupski, Jens; David, Sammy; Lösch, Mathias (2013): 2012 Census of Open Access Repositories in Germany. fig<strong>share</strong>. <br /> http://dx.doi.org/10.6084/m9.figshare.677099</p>
Data of the Open Access Repository Ranking 2015
<p>The Open Access Repository Ranking 2015 ranks open access repositories from Germany, Austria and Switzerland. Data for the 2015 ranking was partly submitted by the respective repository managers, and partly automatically validated via the OAI interfaces. The OARR team reviewed all submissions assuring the quality and validity.<br> The ranking is based on an open and transparent metric that was developed in accordance with the open access community. This metric is a synthesis of different schemes and studies that surveyed and describe open access repositories.<br> Data includes the 2015 scores and descriptive information on the repositories as well as the 2015 metric.</p>
The Landscape of Research Data Repositories in 2015. A re3data Analysis
<p>The attached data sets provides an overview of the landscape of research data repositories in 2015. They are based on an analysis of the re3data - registry of research data repositories from December 2015.</p>
Data repository of multi-temporal high-resolution data products of ecosystem structure derived from country-wide airborne laser scanning surveys of the Netherlands
<p><span lang="EN-GB">This data repository contains a set of multi-temporal data products of ecosystem structure derived from four national ALS surveys of the Netherlands (AHN1–AHN4) (folders:<strong> 1_AHN1, 2_AHN2, 3_AHN3, and 4_AHN4</strong>). Four sets of 25 LiDAR-derived vegetation metrics representing ecosystem height, cover, and structural variability are provided at 10 m spatial resolution, providing valuable data sources for a wide range of ecological research and field beyond. A preview of all generated LiDAR metrics are also provided (folder: <strong>5_Maps</strong>). All 25 LiDAR metrics were calculated using Laserfarm workflow (<a href="https://laserfarm.readthedocs.io/en/latest/">https://laserfarm.readthedocs.io/en/latest/</a>) (building on the user-extendable features from the “Laserchicken” software: <a href="https://laserchicken.readthedocs.io/en/latest/#features">https://laserchicken.readthedocs.io/en/latest/#features</a>). All metrics are calculated with the normalized point cloud. More details on metric calculation are provided on GitHub (Laserchicken: <a href="https://github.com/eEcoLiDAR/laserchicken">https://github.com/eEcoLiDAR/laserchicken</a> and Laserfarm: <a href="https://github.com/eEcoLiDAR/Laserfarm">https://github.com/eEcoLiDAR/Laserfarm</a>), as well as on the “Laserchicken” documentation page (<a href="https://laserchicken.readthedocs.io/en/latest/">https://laserchicken.readthedocs.io/en/latest/</a>). We also provided masks to minimize the influence of water surfaces, buildings and roads, powerlines and NA values in the data products (folder: <strong>6_Masks</strong>). To supplement the generated data products, we also provided a set of raster layers that contains point/pulse density of each AHN survey and the DTM and DSM raster layers for each AHN dataset (folder: <strong>7_Auxiliary_data</strong>). To test the robustness of the LiDAR metrics, we also compared the metrics generated from different pulse densities across different habitat types (folder: <strong>8_Sensitivity_analysis</strong>). Two use cases demonstrated the utility of the presented data products: (use case 1) monitoring forest structural change across time using multi-temporal ALS data and (use case 2) comparison of vegetation structural difference within Natura 2000 sites. The used data are also provided (folder: <strong>9_Use_case</strong>). Note that all the raster layers are provided at 10 m resolution under the local Dutch coordinate system “RD_new” (EPSG: 28992, NAP:5709). To gain more insights of the pre-classification accuracy of the AHN datasets, we also conducted a preliminary assessment of the effect of terrain filtering on vegetation change detection across AHN datasets (i.e. AHN2–AHN4). The data used in this analysis are made available (folder: <strong>10_Ground_classification</strong>). </span></p> <p><span lang="EN-GB">An overview of all the folders in the repository:</span></p> <p><strong><span lang="EN-GB">1. </span></strong><strong><span lang="EN-GB">AHN1</span></strong></p> <p><strong><span lang="EN-GB">2. </span></strong><strong><span lang="EN-GB">AHN2</span></strong></p> <p><strong><span lang="EN-GB">3. </span></strong><strong><span lang="EN-GB">AHN3</span></strong></p> <p><strong><span lang="EN-GB">4. </span></strong><strong><span lang="EN-GB">AHN4</span></strong></p> <p><strong><span lang="EN-GB">5. </span></strong><strong><span lang="EN-GB">Maps</span></strong></p> <p><span lang="EN-GB">Those folders contain four sets of 25 LiDAR metrics at 10 m resolution generated from each AHN dataset. The file names and their corresponding LiDAR metrics can be found in Table 1. An additional folder (5_Maps) contains the maps (.pdf format) of all 25 metrics for each AHN dataset.</span></p> <p><strong><span lang="EN-GB">6. Masks</span></strong></p> <ul> <li><span lang="EN-GB">ahn3_10m_mask_building_road_water.tif</span></li> <li><span lang="EN-GB">ahn4_10m_mask_building_road_water.tif</span></li> <li><span lang="EN-GB">ahn4_10m_mask_powerline.tif</span></li> <li><span lang="NL">ahn1_10m_NA_mask.tif</span></li> <li><span lang="NL">ahn2_10m_NA_mask.tif</span></li> <li><span lang="NL">ahn3_10m_NA_mask.tif</span></li> <li><span lang="NL">a</span><span lang="NL">hn4_10m_NA_mask.tif</span></li> </ul> <p><span lang="NL"> </span></p> <p><span lang="EN-GB">It contains two mask layers of water surfaces, buildings and roads for both AHN3 and AHN4 data products based on the Dutch cadaster data (TOP10NL) from 2018 (corresponding to AHN3) and 2021 (corresponding to AHN4) (<a href="https://www.kadaster.nl/zakelijk/producten/geo-informatie/topnl">https://www.kadaster.nl/zakelijk/producten/geo-informatie/topnl</a>). In the masks, water surfaces, buildings and roads were merged into one class with pixel value assigned to 1 and the rest has the pixel value of 0. There is also a powerline mask generated from the AHN4 dataset at 10 m resolution, where pixels containing powerlines were assigned a value of 1 and the rest as NoData. We provide those masks to minimize the inaccuracies of the data products caused by human infrastructures and water surfaces. We also provided a mask for each AHN dataset where NA value occurs — areas with no vegetation points (“unclassified” class in the AHN datasets). Pixels with NA value were assigned with a value of 1 and the rest as 0.</span></p> <p><strong><span lang="EN-GB">7. Auxiliary data</span></strong></p> <p><span lang="EN-GB">(1) Point_density</span></p> <ul> <li><span lang="EN-GB">ahn1_10m_point_density.tif</span></li> <li><span lang="EN-GB">ahn2_10m_point_density.tif</span></li> <li><span lang="EN-GB">ahn3_10m_point_density.tif</span></li> <li><span lang="EN-GB">ahn4_10m_point_density.tif</span></li> </ul> <p><span lang="EN-GB">(2) Pulse_density</span></p> <ul> <li><span lang="EN-GB">ahn3_10m_pulse_density.tif</span></li> <li><span lang="EN-GB">ahn4_10m_pulse_density.tif</span></li> </ul> <p><span lang="EN-GB">(3) Flighttime</span></p> <ul> <li><span lang="EN-GB">ahn3_10m_flighttime.tif</span></li> <li><span lang="EN-GB">ahn4_10m_flighttime.tif</span></li> </ul> <p><span lang="EN-GB">(4) DTM_DSM</span></p> <ul> <li><span lang="EN-GB">ahn2_10m_dtm.tif</span></li> <li><span lang="EN-GB">ahn2_10m_dsm.tif</span></li> <li><span lang="EN-GB">ahn3_10m_dtm.tif</span></li> <li><span lang="EN-GB">ahn3_10m_dsm.tif</span></li> <li><span lang="EN-GB">ahn4_10m_dtm.tif</span></li> <li><span lang="EN-GB">ahn4_10m_dsm.tif</span></li> </ul> <p><span lang="EN-GB">It contains four raster layers representing the point density of each AHN dataset, two raster layers for pulse density of the AHN3 and AHN4, two raster layers for flight timestamp of the AHN3 and AHN4, and six DTM and DSM layers for AHN2</span><span lang="EN-GB">–</span><span lang="EN-GB">AHN4. All raster layers are provide at 10 m resolution.</span></p> <p><strong><span lang="EN-GB">8. Sensitivity analysis</span></strong></p> <ul> <li><span lang="EN-GB">Dunes</span></li> <li><span lang="EN-GB">Marsh</span></li> <li><span lang="EN-GB">Grassland</span></li> <li><span lang="EN-GB">Shrubland</span></li> <li><span lang="EN-GB">Woodland</span></li> <li><span lang="EN-GB">Code</span></li> <li><span lang="EN-GB">Figure</span></li> </ul> <p><span lang="EN-GB">It contains the 25 metrics generated from point clouds with the original and down-sampled pulse densities (original pulse density of the AHN4, pulse density of the AHN3, ½ of the pulse density of the AHN3, and ¼ of the pulse density of AHN3) for each habitat type (i.e. dunes, marsh, grassland, shrubland, and woodland). We also provided the code and the figures generated from this analysis.</span></p> <p><strong><span lang="EN-GB">9. Use_case</span></strong></p> <p><span lang="EN-GB">(1) Multi-temporal_AHN</span></p> <ul> <li><span lang="EN-GB">Data</span></li> <li><span lang="EN-GB">Usecase_multi-temporal_AHN.R</span></li> </ul> <p><span lang="EN-GB">It contains the input data for the use case data processing (i.e. Data folder), including the shapefile of the area (i.e. shp folder), and extracted pixel value from six selected LiDAR metrics from AHN1–AHN5 (i.e. Metrics folder), and the selected LiDAR metrics of the area (e.g. Hp95 folder), and the R code for data processing (i.e. Usecase_multi-temporal_AHN.R). </span></p> <p><span lang="EN-GB">(2) Natura2000</span></p> <ul> <li><span lang="EN-GB">Data</span></li> <li><span lang="EN-GB">Natura2000_end2021_HABITATCLASS.csv</span></li> <li><span lang="EN-GB">Natura2000_NL_habitat_grouped.csv</span></li> <li><span lang="EN-GB">Usecase_Natura2000.R</span></li> </ul> <p><span lang="EN-GB">It contains a folder of the input data used for the use case (i.e. Data folder), including the shapefile (i.e. shp folder) of the Natura 2000 sites in the Netherlands (i.e. Nature2000_NL_RDnew.shp) and the 100 random sample plots from each habitat type (e.g. woodland_points.shp), and the LiDAR metrics from AHN4 used for demonstrating the vegetation structure within each habitat type (i.e. AHN4_metrics folder). The table “Natura2000_end2021_HABITATCLASS.csv” is the original attribute table of Natura 2000 sites, including information related to the description of habitat classes (column “DESCRIPTION”), the code corresponding to the habitat class (column “HABITATCODE”), the code for the specific site (column “SITECODE”), and the percentage of the cover of a specific habitat class in one site (column “PERCENTAGECOVER”). The table “Natura2000_NL_habitat_grouped.csv” contains two subtabs, one (i.e. “Habitatclass”) is the copy of the original attribute table of Natura 2000 sites in the Netherlands, and the other one (i.e. “Habitat_class_summary”) is the grouped habitat type based on the dominant habitat class (i.e. class with the highest percentage cover) in each site. Different colors indicate different habitat types, corresponding to the colors in the first tab (“Habitatclass”) where the dominant habitat class was highlighted for each site. </span></p> <p><strong><span lang="EN-GB">10. Ground classification</span></strong></p> <ul> <li><span lang="EN-GB">Raw_point_cloud</span></li> <li><span lang="EN-GB">Computed_metrics </span></li> <li><span lang="EN-GB">Plottings_and_code</span></li> <li><span lang="EN-GB">ArcGIS_project</span></li> </ul> <p><span lang="EN-GB">It contains four subfolders: (1) The original point cloud for each sample area (AHN2–AHN4) (subfolder: Raw_point_cloud); (2) The 25 LiDAR metrics computed from the original point clouds with pre-classification of AHN and from the new terrain filtering method across AHN2–AHN4 (subfolder: Computed_metrics); (3) Generated violin plots for the comparison of vegetation change detection and the python code employed (subfolder: Plottings_and_code); (4) an ArcGIS project which the shapefiles of the study area and sample plots are provided (subfolder: ArcGIS_project).</span></p> <p><strong><span lang="EN-GB">Code availability</span></strong></p> <p><span lang="EN-GB">Jupyter Notebooks for processing AHN datasets: </span></p> <p><span lang="EN-GB"><a href="https://github.com/ShiYifang/AHN">https://github.com/ShiYifang/AHN</a></span></p> <p><span lang="EN-GB">Laserfarm workflow repository: </span></p> <p><span lang="EN-GB"><a href="https://github.com/eEcoLiDAR/Laserfarm">https://github.com/eEcoLiDAR/Laserfarm</a></span></p> <p><span lang="EN-GB">Laserchicken software repository: </span></p> <p><span lang="EN-GB"><a href="https://github.com/eEcoLiDAR/laserchicken">https://github.com/eEcoLiDAR/laserchicken</a></span></p> <p><span lang="EN-GB">Code for downloading AHN dataset: <a href="https://github.com/ShiYifang/AHN/tree/main/AHN_downloading">https://github.com/ShiYifang/AHN/tree/main/AHN_downloading</a></span></p> <p><span lang="EN-GB">Code for generating masks for AHN datasets: <a href="https://github.com/ShiYifang/AHN/tree/main/AHN_masks">https://github.com/ShiYifang/AHN/tree/main/AHN_masks</a></span></p> <p><span lang="EN-GB">Code for demonstration of ecological use cases: <a href="https://github.com/ShiYifang/AHN/tree/main/Use_case">https://github.com/ShiYifang/AHN/tree/main/Use_case</a></span></p> <p> </p>
Image Repository Decision Tree - Where do I deposit my imaging data
<p>Depositing data in quality data repositories is one crucial step towards FAIR (Findable, Accessible, Interoperable, and Reusable) data. Accordingly, Euro-BioImaging strongly encourages sharing scientific imaging data in established, thematic repositories. </p> <p>To guide you in the selection of appropriate repositories, we have created an overview of available repositories for different types of image data, including their scope and requirements. This decision tree guides you through questions about your data and directs you to the correct repository, and/or provides instructions for further processing to meet the critera of the repositories. </p> <p>Three seperate trees are provided for different classes of imaging data: open bioimage data, preclinical data, and human imaging data. These versions with three trees can be used for web-view. Update: also the editable versions in powerpoint format (.pptx) are now provided. Please be aware that opening the versions with another program might lead to shifted formatting.</p> <p>Update: we now also provide ready-to-print versions designed to be printed on A3 format. One page shows the open bioimaging data tree and one page combines the preclinical and human imaging data trees. Also the editable versions of these are provided.</p>
CGM Scoping Review Data Repository
<p>This dataset represents the data extracted as part of a CGM-based biological feedback scoping review.</p>
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.