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Comparison of high-resolution global canopy height maps and their applicability to biodiversity modelling - dataset
<p>This repository was created to provide datasets related with an article comparing high-resolution global canopy height maps and exploring their applicability to biodiversity modeling in temperate biomes.</p> <p>EBR stands for Entlebuch Biosphere Reserve, MRF stands for Mount Richmond Forest and TAW stands for Trinity Alps Wilderness.</p> <p>The original airborne laser scanning point clouds used for the generation of the canopy height models were sourced from the LINZ Data Service and OpenTopography, and licensed for reuse under the CC BY 4.0 licence (<a href="https://mcas-proxyweb.mcas.ms/certificate-checker?login=false&originalUrl=https%3A%2F%2Fdoi.org.mcas.ms%2F10.5069%2FG97D2SB0%3FMcasTsid%3D20893&McasCSRF=cf3ae9aed6f2016d3ceedda452d422646f4f8e5a5e6270380b370aad4964323a">https://doi.org/10.5069/G97D2SB0</a>); Federal Office of Topography swisstopo (<a href="https://mcas-proxyweb.mcas.ms/certificate-checker?login=false&originalUrl=https%3A%2F%2Fwww.swisstopo.admin.ch.mcas.ms%2Fen%2Fgeodata%2Fheight%2Fsurface3d.html%3FMcasTsid%3D20893&McasCSRF=cf3ae9aed6f2016d3ceedda452d422646f4f8e5a5e6270380b370aad4964323a">https://www.swisstopo.admin.ch/en/geodata/height/surface3d.html</a>); and U.S. Geological Survey (<a href="https://mcas-proxyweb.mcas.ms/certificate-checker?login=false&originalUrl=https%3A%2F%2Fapps.nationalmap.gov.mcas.ms%2Fdownloader%2F%3FMcasTsid%3D20893&McasCSRF=cf3ae9aed6f2016d3ceedda452d422646f4f8e5a5e6270380b370aad4964323a">https://apps.nationalmap.gov/downloader/</a>).</p> <p>The Global Forest Canopy Height Map - GFCH (Potapov et al. 2021; https://glad.umd.edu/dataset/gedi) and the high-resolution canopy height model of the Earth - HRCH (Lang et al. 2022, https://langnico.github.io/globalcanopyheight/) are provided free of charge, without restriction of use under Creative Commons Attribution 4.0 International License. Publications, models, and data products that make use of these datasets must include proper acknowledgement.</p> <p><em>P. Potapov, X. Li, A. Hernandez-Serna, A. Tyukavina, M.C. Hansen, A. Kommareddy, A. Pickens, S. Turubanova, H. Tang, C.E. Silva, J. Armston, R. Dubayah, J. B. Blair, M. Hofton (2021) Mapping and monitoring global forest canopy height through integration of GEDI and Landsat data. Remote Sensing of Environment, 112165. <a href="https://doi.org/10.1016/j.rse.2020.112165">https://doi.org/10.1016/j.rse.2020.112165</a></em></p> <p><em>Lang, N., Jetz, W., Schindler, K., & Wegner, J. D. (2022). A high-resolution canopy height model of the Earth. arXiv preprint arXiv:2204.08322.</em></p> <p>R scripts related with this datasets are available at Github (https://github.com/lukasgabor/Comparison-of-high-resolution-global-canopy-height-maps-and-their-applicability; <a href="https://doi.org/10.5281/zenodo.7332716">DOI: 10.5281/zenodo.7332716</a>)</p> <p>In the previous version (1.0) the average was calculated for the canopy height. In this version (1.1), the maximum height is calculated for the canopy height.</p>
Global mangrove soil carbon data set at 30 m resolution for year 2020 (0-100 cm)
<p>Global soil organic carbon stocks in mangrove forests at 30 m resolution, and predicted for 2020 using spatiotemporal ensemble machine learning. Soil organic carbon stock (t/ha) was derived using predictions of soil organic carbon content and bulk density (BD) to 1 m soil depth, which were then aggregated to calculate soil organic carbon stocks.</p> <p>The "mangroves_tiles_SOC_predictions_2020.zip" file contains predictions of SOC content, Bulk Density (BD) and aggregated SOC stocks (t/ha) for 0—100 cm depth interval. Example of a tile:</p> <ul> <li>089E_21N (89E to 90E, 21N to 22N): <ul> <li>sol_db.od_mangroves.typology_m_30m_s0..100cm_2020_global_v0.1.tif = predicted BD aggregated to 0—100 cm;</li> <li>sol_soc.wpct_mangroves.typology_m_30m_s0..0cm_2020_global_v1.1.tif = predicted SOC content (%) at 0 cm depth (surface soil);</li> <li>sol_soc.wpct_mangroves.typology_m_30m_s0..100cm_2020_global_v1.1.tif = predicted SOC content (%) for 0—100 cm;</li> <li>sol_soc.tha_mangroves.typology_m_30m_s0..100cm_2020_global_v0.1.tif = predicted SOC stocks in t/ha (mean value);</li> <li>sol_soc.tha_mangroves.typology_l.std_30m_s0..100cm_2020_global_v0.1.tif = predicted SOC stocks in t/ha lower 95% probability prediction interval;</li> <li>sol_soc.tha_mangroves.typology_u.std_30m_s0..100cm_2020_global_v0.1.tif = predicted SOC stocks in t/ha upper 95% probability prediction interval;</li> </ul> </li> </ul> <p>Example of a tile:</p> <ul> <li>class : RasterLayer</li> <li>dimensions : 4004, 4004, 16032016 (nrow, ncol, ncell)</li> <li>resolution : 0.00025, 0.00025 (x, y)</li> <li>extent : 88.9995, 90.0005, 20.9995, 22.0005 (xmin, xmax, ymin, ymax)</li> <li>crs : +proj=longlat +datum=WGS84 +no_defs</li> <li>source : sol_db.od_mangroves.typology_m_30m_s0..0cm_2002_global_v0.1.tif</li> </ul> <p>To load global mosaics <strong><strong>Soil Carbon t/ha Maps (0—100cm)</strong></strong> as COGs directly into QGIS or similar, best use:</p> <ul> <li> <p><a href="https://s3.eu-central-1.wasabisys.com/openlandmap/mangroves/sol/soc.tha_tnc.mangroves.typology_m_30m_b0..100cm_2019_2020_go_epsg.4326_v1.2.tif">https://s3.eu-central-1.wasabisys.com/openlandmap/mangroves/sol/soc.tha_tnc.mangroves.typology_m_30m_b0..100cm_2019_2020_go_epsg.4326_v1.2.tif</a></p> </li> <li> <p><a href="https://s3.eu-central-1.wasabisys.com/openlandmap/mangroves/sol/soc.tha_tnc.mangroves.typology_l.std_30m_b0..100cm_2019_2020_go_epsg.4326_v1.2.tif">https://s3.eu-central-1.wasabisys.com/openlandmap/mangroves/sol/soc.tha_tnc.mangroves.typology_l.std_30m_b0..100cm_2019_2020_go_epsg.4326_v1.2.tif</a></p> </li> <li> <p><a href="https://s3.eu-central-1.wasabisys.com/openlandmap/mangroves/sol/soc.tha_tnc.mangroves.typology_u.std_30m_b0..100cm_2019_2020_go_epsg.4326_v1.2.tif">https://s3.eu-central-1.wasabisys.com/openlandmap/mangroves/sol/soc.tha_tnc.mangroves.typology_u.std_30m_b0..100cm_2019_2020_go_epsg.4326_v1.2.tif</a></p> </li> </ul>
An analyst-created, high-resolution seismic arrival time dataset for evaluating machine learning phase detectors
<p>This data set contains phase arrival times and phase labels for one hour of continuous seismic data recorded at the three-component broadband station WY.YNR on 2014 30 March from 13:00:00 to 14:00:00 UTC. This hour of data follows a M<sub>w</sub> 4.8 occurring at 12:34 UTC in the Yellowstone region and contains many small events close together in space and time. All 687 picks (404 P and 283 S) were made by a seismic analyst trained at the University of Utah Seismograph Stations. The goal was to pick as many reasonable arrivals as possible for evaluating the performance of machine-learning-based phase detectors on continuous data during high seismicity rates. Phase picks were made using the Seismic Analysis Code (SAC; Goldstein and Snoke, 2005) and Pyrocko (Heimann <em>et al</em>., 2017). In general, a 1 to 17 Hz bandpass filter was used.</p> <p>The csv file contains the pick id, phase arrival time in UTC and Unix epoch formats, and the phase labels (P or S).</p>
CLM/CTSM glacier input datasets used for study on evaluation variable-resolution CESM2 in High-Mountain Asia
<p><strong>General Info</strong></p> <p>This data archive contains the updated glacier-cover and glacier regions for the Community Land Model version 5 (CLM5)/Community Terrestrial Systems Model (CTSM). The updated glacier-cover and glacier regions are used for a study on the evaluation of variable-resolution (VR) CESM2 in High Mountain Asia (<a href="https://tc.copernicus.org/preprints/tc-2022-256/">https://tc.copernicus.org/preprints/tc-2022-256/</a>). The data archive also contains the model scripts and input files that have been used to create the glacier-cover dataset. The global glacier outlines used for the glacier-cover dataset were retrieved from the Randolph Glacier Inventory version 6 (RGI-Consortium, 2017). The vector data for the Greenland and Antarctic ice sheets were retrieved from the masks of Bedmachine version 4 (Morlighem et al., 2017, 2021) and version 2 (Morlighem et al., 2020; Morlighem, 2020), respectively. </p> <p><strong>Contact</strong></p> <p>René Wijngaard (<a href="mailto:r.r.wijngaard.uu@gmail.com">r.r.wijngaard.uu@gmail.com</a> / <a href="mailto:r.r.wijngaard@uu.nl">r.r.wijngaard@uu.nl</a>) </p> <p><strong>Dataset Contents </strong></p> <pre><code>mksrf_glacier_3x3min_simyr2000.c210708.nc</code></pre> <p>The updated glacier-cover dataset, encompassing three 3-minute datasets: 1) fractional land ice coverage, including both glaciers and ice sheets (PCT_GLACIER), 2) distributions of areal glacier coverage by elevation (PCT_GLC_GIC), and 3) distributions of areal ice-sheet coverage by elevation (PCT_GLC_ICESHEET).</p> <pre><code>mksrf_GlacierRegion_10x10min_nomask_c200813.nc</code></pre> <p>The updated glacier regions, encompassing five different glacier regions (0 - Other regions, 1 - Inside standard CISM grid but outside Greenland itself, 2 - Greenland, 3 - Antarctica, and 4 - High Mountain Asia (new)), used to set the ice melt and runoff behaviour in CLM5/CTSM (more detailed information can be found in the CLM5 Documentation, <a href="https://escomp.github.io/ctsm-docs/">https://escomp.github.io/ctsm-docs/</a>)</p> <pre><code>model_scripts.tar</code></pre> <p>Model scripts used for creating the glacier-cover dataset. A README file is included that lists instructions on how to make the glacier-cover dataset. </p> <pre><code>glacier_final.tar</code></pre> <p>Input files used to create the glacier-cover dataset. The following files are included: a global 30-arcsec merged BedMachine/GMTED2010 elevation dataset (gmted_bedmachine_stitched.nc) and land-sea mask (gmted2010_modis-rawdata-lonshift.nc), Antarctica land mask (BedMachineAntarcticaRotate2RotateBack_2020-07-15_v02_lonshift.map_TO_30arcsec.nc), Greenland land mask (BedMachineGreenland-2021-04-20.map_TO_30arcsec.nc), and 30-arcsec datasets encompassing glacier-cover (30arcsec_00_rgi60_World.nc) and ice-sheet cover (30arcsec_00_BM_World.nc).</p>
Biodiversity Index, in 2019 and across RCP 4.5, and 8.5 scenarios in 2050 and 2100 of 1508 European Marine Species based on ensemble Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution
<p>Biodiversity Index in 2019 and across RCP 4.5, and 8.5 scenarios in 2050 and 2100 of 1508 European marine species based on ensemble Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution. The Index counts the number of species (among the 1508) potentially present in each 0.5° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
CNBH-10 m: A first Chinese building height at 10 m resolution
<p>Building height is a crucial variable in the study of urban environments, regional climates, and human-environment interactions. However, high-resolution data on building height, especially at the national scale, are limited. Fortunately, high spatial-temporal resolution earth observations, harnessed using a cloud-based platform, offer an opportunity to fill this gap. We describe an approach to estimate 2020 building height for China at 10 m spatial resolution based on all-weather earth observations (radar, optical, and night light images) using the Random Forest (RF) model. Results show that our building height simulation has a strong correlation with real observations at the national scale (RMSE of 6.1 m, MAE = 5.2 m, <em>R</em> = 0.77). The Combinational Shadow Index (CSI) is the most important contributor (15.1%) to building height simulation. Analysis of the distribution of building morphology reveals significant differences in building volume and average building height at the city scale across China. <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/macao">Macau</a> has the tallest buildings (22.3 m) among Chinese cities, while Shanghai has the largest building volume (298.4 10<sup>8</sup> m<sup>3</sup>). The strong correlation between modelled building volume and socio-economic parameters indicates the potential application of building height products. The building height map developed in this study with a resolution of 10 m is open access, provides insights into the 3D morphological characteristics of cities and serves as an important contribution to future urban studies in China.</p>
Ecological Niche Models of 96 European Marine Species, for 2019, developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines at 0.1° Resolution
<p>Native ecological niche models of 96 European marine species of particular commercial and conservation interest developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines, for 2019 at 0.1° spatial resolution.</p>
Ensemble Ecological Niche Models and Biodiversity Index for 2019 of 96 European Marine Species based on Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, AquaMaps, and Support Vector Machines at 0.1° Resolution
<p>Ensemble Ecological Niche Models for 2019 of 96 European marine species of particular commercial and conservation interest, based on Ecological Niche Models developed with (i) Artificial Neural Networks, (ii) Maximum Entropy, (iii) Support Vector Machines, and (iv) AquaMaps at 0.1° Resolution. The data report, for each 0.1° cell, how many models (from 0 to 4) overcome a model-specific decision threshold to assess species presence in the cell. A Biodiversity Index is also provided as the count of the number of species (among the 96) potentially present in each 0.1° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
WRF Forecast Data used for Verification of multi-resolution model forecasts of heavy rainfall events of 23rd-26th August 2017 over Nigeria
<p>A deterministic Weather Research and Forecasting model version 4.2 forecast of heavy convective rainfall associated with the passage of the African Easterly Wave (AEW) within the period 23<sup>rd</sup>-26<sup>th</sup> August 2017 over Nigeria. The model was setup to perform two nested domain simulations with 18 (parent domain), 6 and 2 km (hereafter WRF18, WRF6 and WRF2) horizontal resolutions. The outer domain covers West Africa and the innermost domain, which runs at convection-permitting scale, focuses on Nigeria. When interpreting the results, it is worthy of note that the data has been regridded to 18 km, which is 3 x the grid scale for WRF6 and 9 x the grid scale for WRF2. This means that there is a fair degree of smoothing that has been applied using a bilinear regridding process to get the models onto a level playing field. Only WRF18 retains its native grid and has not benefited from any additional smoothing.</p> <p>The WRF model setup is similar to the study of Gbode et al. (2019; DOI: https://doi.org/10.1007/s00704-018-2538-x) in terms of the model physics combination used in the model simulations. The parameterization schemes used are the Goddard (GD) WRF model microphysics (MP), the Mellor–Yamada–Janjic (MYJ) planetary boundary layer (PBL) and the Bett-Miller-Janjic (BMJ) cumulus convection (CU) parameterization schemes. This combination was found to reproduce realistic rainfall and temperature relative to gridded observations over West Africa. The GD is a six-class microphysics with graupel and modifications for ice/water saturation. MYJ is a local closure scheme that predicts turbulent kinetic energy and the BMJ CU is a profile adjustment scheme that relaxes both deep and shallow profiles toward a reference profile without explicit updraft, downdraft, or cloud entrainment. However, the CU scheme was turned off in the 2 km domain to explicitly represent convection.</p>
Pan-EU Landmask: 10m Resolution Geospatial Land Coverage with Administrative Boundary details on country and regional level
<p><strong>Pan-EU Land Mask Summary</strong></p> <p>Considering the land mask for pan-EU, we will closely match the data coverage of <a href="https://land.copernicus.eu/pan-european">https://land.copernicus.eu/pan-european</a> i.e. the official selection of countries listed here: <a href="https://land.copernicus.eu/portal_vocabularies/geotags/eea39">https://lanEEA39d.copernicus.eu/portal_vocabularies/geotags/eea39</a>.</p> <p>There are a total of three landmask files available, each of which is aligned with the standard spatial/temporal resolution and sizes of <a href="https://ai4soilheath.eu">AI4SoilHealth</a> Data Cube specifications, which is: Xmin = 900,000, Ymin = 899,000, Xmax = 7,401,000, Ymax = 5,501,000, with Coordinate reference system of epsg:3035. Additionally, these files include a corresponding look-up table that provides explanations for the values present in the raster data. The scripts used to generate these masks can be found <a href="https://github.com/AI4SoilHealth/SoilHealthDataCube/tree/main/paneu_landmask">here</a>.</p> <p>The masks are:</p> <ol> <li> <p>Landmask</p> </li> <li> <p>ISO-code country mask</p> </li> <li> <p>NUTS3 mask</p> </li> </ol> <p><strong>Name convention</strong></p> <p>To ensure consistency and ease of use across and within the projects, the files here are named according to the standard OpenLandMap file-naming convention. The OpenLandMap file-naming convention works with 10 fields that basically define the most important properties of the data, this way users can search files, prepare data analysis etc, without even needing to access or open files. The 10 fields include:</p> <ol> <li> <p>Generic variable name: country.code</p> </li> <li> <p>Variable procedure combination i.e. method standard (standard abbreviation): iso.3166</p> </li> <li> <p>Position in the probability distribution / variable type: c</p> </li> <li> <p>Spatial support (usually horizontal block) in m or km: 30m</p> </li> <li> <p>Depth reference or depth interval e.g. below ("b"), above ("a") ground or at surface ("s"): s</p> </li> <li> <p>Time reference begin time (YYYYMMDD): 20210101</p> </li> <li> <p>Time reference end time: 20211231</p> </li> <li> <p>Bounding box (2 letters max): eu </p> </li> <li> <p>EPSG code: epsg.3035</p> </li> <li> <p>Version code i.e. creation date: v20230722</p> </li> </ol> <p>An example of a file-name based on the description above:</p> <p><em>country.code_iso.3166_c_100m_s_20210101_20211231_eu_epsg.3035_v20230722</em></p> <p><strong>Landmask</strong></p> <p>The basic principle to create the land mask is to include as much as land as possible, to avoid missing any land pixels and ensure precise differentiation between land, ocean and inland water bodies.</p> <p>Two reference datasets are used, </p> <ol> <li> <p><a href="https://esa-worldcover.org/en">WorldCover</a>, 10 m resolution.</p> </li> <li> <p><a href="https://www.mapsforeurope.org/datasets/euro-global-map">EuroGlobalMap</a>, with shapefiles of administrative boundaries, inland water bodies, ocean and landmask.</p> </li> </ol> <p>When generating the land mask, the two reference datasets in a way that:</p> <ul> <li> <p>If either of the two reference datasets identifies a pixel as land, it is considered a land pixel in our mask. </p> </li> <li> <p>Regarding ocean and inland water bodies, a pixel is classified as a water pixel only when both reference datasets confirm its identification as water.</p> </li> </ul> <p>The landmask consists of 4 values:</p> <ul> <li> <p>10: not in the pan-EU area, i.e. out of mapping scope</p> </li> <li> <p>1: land</p> </li> <li> <p>2: inland water</p> </li> <li> <p>3: ocean</p> </li> </ul> <p>This landmask is available in 10m, 30m, 100m, 250m, and 1km resolution formats respectively. The coarse resolution landmasks (>10 m) are generated by resampling from the 10m resolution base map using resampling method “min” in GDAL. This “min” method allows taking the minimum values from the contributing pixels, to keep as much land as possible.</p> <p><strong>ISO-3166 country code mask</strong></p> <p>This ISO-3166 country code mask is created from <a href="https://www.mapsforeurope.org/datasets/euro-global-map">EuroGlobalMap</a> country shapefile. This mask is available in 10m, 30m and 100m resolution. In this raster file, each country is assigned a unique value, which allows for the interpretation and analysis of data associated with a specific country.</p> <p>The values are assigned to each country according to iso-3166 country code, which can be found in the corresponding look-up table. The coarse resolution masks (>10 m) are generated by resampling from the 10m resolution base map using resampling method “mode” in GDAL.</p> <p><strong>NUTS-3 mask</strong></p> <p>The nuts-3 code mask is created from the European NUTS3 shapefile. In this raster file, each unique NUT3 level area is assigned a unique value, which allows for the interpretation and analysis of data associated with specific NUTS3 regions.</p> <p>The values of pixels and its associated meanings can be found in the corresponding look-up table. This nut-3 code mask is available in 10m, 30m and 100m resolution formats. The coarse resolution masks (>10 m) are generated by resampling from the 10m resolution base map using resampling method “mode” in GDAL.</p> <p>It should be noted that the ISO-code country mask covers a more extensive area compared to the NUTS3 mask. This broader coverage includes countries like Ukraine and others beyond the NUTS3 mask, while NUTS mask shows more details about regional administrative boundaries.</p>
Data for: World's human migration patterns in 2000-2019 unveiled by high-resolution data
<p> </p> <p>This dataset provides a<strong> global gridded (5 arc-min resolution) detailed annual net-migration dataset for 2000-2019</strong>. We also provide global annual birth and death rate datasets – that were used to estimate the net-migration – for same years. The dataset is presented in details, with some further analyses, in the following publication. <strong><em>Please cite this paper when using data. </em></strong></p> <p>Niva et al. 2023. World's human migration patterns in 2000-2019 unveiled by high-resolution data. Nature Human Behaviour 7: 2023–2037. Doi: <a href="https://doi.org/10.1038/s41562-023-01689-4" target="_blank" rel="noopener">https://doi.org/10.1038/s41562-023-01689-4</a> </p> <p>You can explore the data in our online net-migration explorer: <a href="https://wdrg.aalto.fi/global-net-migration-explorer/" target="_blank" rel="noopener">https://wdrg.aalto.fi/global-net-migration-explorer/</a></p> <p> </p> <p><strong>Short introduction to the data</strong></p> <p>For the dataset, we collected, gap-filled, and harmonised: </p> <ol> <li>a comprehensive national level birth and death rate datasets for altogether 216 countries or sovereign states; and </li> <li>sub-national data for births (data covering 163 countries, divided altogether into 2555 admin units) and deaths (123 countries, 2067 admin units).</li> </ol> <p>These birth and death rates were downscaled with selected socio-economic indicators to 5 arc-min grid for each year 2000-2019. These allowed us to calculate the 'natural' population change and when this was compared with the reported changes in population, we were able to estimate the annual net-migration. See more about the methods and calculations at Niva et al (2023). </p> <p><strong><em>We recommend using the data either over multiple years (we provide 3, 5 and 20 year net-migration sums at gridded level) or then aggregated over larger area (we provide adm0, adm1 and adm2 level geospatial polygon files). This is due to some noise in the gridded annual data. </em></strong></p> <p>Due to copy-right issues we are not able to release all the original data collected, but those can be requested from the authors. </p> <p> </p> <p><strong>List of datasets</strong></p> <p><em>Birth and death rates: </em></p> <p>raster_birth_rate_2000_2019.tif: Gridded birth rate for 2000-2019 (5 arc-min; multiband tif) </p> <p>raster_death_rate_2000_2019.tif: Gridded death rate for 2000-2019 (5 arc-min; multiband tif) </p> <p>tabulated_adm1adm0_birth_rate.csv: Tabulated sub-national birth rate for 2000-2019 at the division to which data was collected (subnational data when available, otherwise national) </p> <p>tabulated_ adm1adm0_death_rate.csv: Tabulated sub-national death rate for 2000-2019 at the division to which data was collected (subnational data when available, otherwise national) </p> <p> </p> <p><em>Net-migration: </em></p> <p>raster_netMgr_2000_2019_annual.tif: Gridded annual net-migration 2000-2019 (5 arc-min; multiband tif) </p> <p>raster_netMgr_2000_2019_3yrSum.tif: Gridded 3-yr sum net-migration 2000-2019 (5 arc-min; multiband tif) </p> <p>raster_netMgr_2000_2019_5yrSum.tif: Gridded 5-yr sum net-migration 2000-2019 (5 arc-min; multiband tif) </p> <p>raster_netMgr_2000_2019_20yrSum.tif: Gridded 20-yr sum net-migration 2000-2019 (5 arc-min) </p> <p> </p> <p>polyg_adm0_dataNetMgr.gpkg: National (adm 0 level) net-migration geospatial file (gpkg) </p> <p>polyg_adm1_dataNetMgr.gpkg: Provincial (adm 1 level) net-migration geospatial file (gpkg) (if not adm 1 level division, adm 0 used) </p> <p>polyg_adm2_dataNetMgr.gpkg: Communal (adm 2 level) net-migration geospatial file (gpkg) (if not adm 2 level division, adm 1 used; and if not adm 1 level division either, adm 0 used) </p> <p> </p> <p><strong>Files to run online net migration explorer </strong></p> <p>masterData.rds and admGeoms.rds are related to our online ‘Net-migration explorer’ tool (<a href="https://wdrg.aalto.fi/global-net-migration-explorer/">https://wdrg.aalto.fi/global-net-migration-explorer/</a>). The source code of this application is available in <a href="https://github.com/vvirkki/net-migration-explorer">https://github.com/vvirkki/net-migration-explorer</a>. Running the application locally requires these two .rds files from this repository. </p> <p> </p> <p><strong>Metadata </strong></p> <p><em>Grids: </em></p> <p>Resolution: 5 arc-min (0.083333333 degrees) </p> <p>Spatial extent: Lon: -180, 180; -90, 90 (xmin, xmax, ymin, ymax) </p> <p>Coordinate ref system: EPSG:4326 - WGS 84 </p> <p>Format: Multiband geotiff; each band for each year over 2000-2019 </p> <p>Units: </p> <ul> <li> <p>Birth and death rates: births/deaths per 1000 people per year </p> </li> <li> <p>Net-migration: persons per 1000 people per time period (year, 3yr, 5yr, 20yr, depending on the dataset) </p> </li> </ul> <p> </p> <p><em>Geospatial polygon (gpkg) files: </em></p> <p>Spatial extent: -180, 180; -90, 83.67 (xmin, xmax, ymin, ymax) </p> <p>Temporal extent: annual over 2000-2019 </p> <p>Coordinate ref system: EPSG:4326 - WGS 84 </p> <p>Format: gkpk </p> <p>Units: </p> <ul> <li> <p>Net-migration: persons per 1000 people per year </p> </li> </ul>
MeteoEurope1km - TMAX (1991–2000): daily gridded meteorological dataset for Europe at a 1-km spatial resolution for the 1991–2020 period
<p>MeteoEurope1km is the daily gridded meteorological dataset for Europe at a 1-km spatial resolution for the 1991–2020 period. The dataset consists of five daily variables:</p> <ul> <li><strong>TMAX - maximum temperature</strong> (<strong>1991–2005 period</strong>, 2006–2020 period)</li> <li>TMIN - minimum temperature (1991–2005 period, 2006–2020 period)</li> <li>TMEAN - mean temperature (1991–2005 period, 2006–2020 period)</li> <li>SLP - mean sea level pressure</li> <li>PRCP - total precipitation</li> </ul> <p>Daily gridded temperature data were interpolated using the Regression Kriging, with digital elevation model (DEM) and topographic wetness index (TWI) as covariates.<br> Daily gridded sea level pressure data were interpolated using Ordinary Kriging.<br> Daily gridded precipitation data were interpolated using Indicator and Ordinary Kriging methodology in two steps:</p> <ol> <li>Indicator Kriging - prediction of precipitation occurence</li> <li>Ordinary Kriging - prediction of total daily precipitation for locations where precipitation occurs (1. step).</li> </ol> <p>File naming convention of the MeteoEurope1km files is <em>var_day_yyyymmdd_proj.tif</em> (e.g. <em>tmax_day_20201231_3035.tif</em>), where:</p> <ul> <li><em>var</em> is a daily meteorological variable name - tmax, tmin, tmean, slp, or prcp</li> <li><em>proj</em> is a dataset projection EPSG code - 3035</li> </ul> <p>Units of the dataset values are</p> <ul> <li>temperature (Tmean, Tmax, and Tmin) - tenths of a degree in the Celsius scale (℃)</li> <li>SLP - tenths of a mbar</li> <li>PRCP - tenths of a mm</li> </ul> <p>All dataset values are stored as integers (INT32 data type) in order to reduce the size of the GeoTIFF files, i.e., temperature values should be divided by 10 to obtain degrees Celsius, and the same for SLP and PRCP to obtain millibars and millimeters.<br> All dataset files are available as Cloud-Optimized GeoTIFFs (COGs).<br> Use the R <a href="https://github.com/AleksandarSekulic/Rmeteo">meteo</a> package, <em>europe1km</em> function to make a point query and obtain the values for a specific location and a specific period.</p>
Underwater surveys of mullet schools (Mugil liza) with Adaptive Resolution Imaging Sonar
<p>This dataset is part of a research project that employs deep learning, with a density-based regression approach, to count fish in low-resolution sonar images (Tarling et al. preprint arXiv DOI: http://arxiv.org/abs/2104.14964).</p> <p>In this repository, we provide data from sonar-based underwater videos of schools of migratory mullets (<em>Mugil liza</em>) recorded at the Tesoura beach (28.495775 S, 48.759996 W), a 100-meter long beach at the inlet canal connecting the Laguna lagoon system to the Atlantic Ocean, in southern Brazil. Since the water transparency at the lagoon canal is very low (from 0.3 to 1.5m visibility; collected <em>in situ</em> with a Secchi disk), mullet schools were recorded by deploying an Adaptive Resolution Imaging Sonar, ARIS 3000 (Sound Metrics Corp, WA, USA), which uses 128 beams to project a wedge-shaped volume of acoustic energy and convert their returning echoes into a digital overhead view of the mullet schools.</p> <p>This dataset contains 500 fully annotated images that were manually marked for the location and abundance of mullet fish, and 126 raw sonar video files, representing over 100k images. The files are organized as follows:</p> <p>1) "2018-MM-DD_HHMMSS" files are mp4 videos (you may need to add the file extension ".mp4"): There are 126 ARIS files converted into MP4 videos totalling over 789MB of underwater footage captured at 3 frames/seconds. Note that file names indicate the date and time the video was recorded.</p> <p>2) ".npy" files (in Labelled_data.zip): From the video files, 500 images were selected for labelling. Images (x) were cropped to represent a 4x8.5m<sup>2</sup> area and resized to 320 x 576 pixels. Mullet fish were marked with a point annotation. Corresponding ground truth density maps (y) were generated by convolving a Gaussian kernel over the image mask, size =4 and standard deviation = 1. The labelled dataset was randomly split into a holdout partition of 350 training images, 70 validation, and 80 test. </p> <p>3) ".csv" files: log of frames selected for the labelled subset of data</p> <p>4) ".h5" file: pre-trained weights for our multi-task with uncertainty regularisation network</p> <p>To advance the development of these machine learning tools, we also make our code openly available (https://github.com/ptarling/DeepLearningFishCounting).</p>
Dataset: Simulation-based parameter optimization for fetal brain MRI super-resolution reconstruction
<p>This dataset contains the data used in the paper</p> <blockquote> <p>de Dumast, P., Sanchez, T., Lajous, H., Bach Cuadra, M. (2023). Simulation-Based Parameter Optimization for Fetal Brain MRI Super-Resolution Reconstruction. MICCAI 2023. LNCS, vol 14226. Springer, Cham. https://doi.org/10.1007/978-3-031-43990-2_32</p> </blockquote> <p>A preprint can also be found on <a href="https://arxiv.org/abs/2211.14274">arXiv</a>. If you found this dataset useful or used it in your research, please cite this reference.</p> <p>This paper studied the impact of the regularization parameter <span class="math-tex">\(\alpha \)</span> on the super-resolution reconstruction of fetal brain magnetic resonance (MR) images. It used simulated T2-weighted data MR images generated using FaBiAN v2.0, a Fetal Brain magnetic resonance Acquisition Numerical phantom that simulates fast spin echo (FSE) sequences of the developing fetal brain throughout gestation. The dataset contains the raw simulated data, the corresponding ground truths as well as corresponding super-resolution (SR) reconstructions using MIALSRTK and NiftyMIC with varying regularization parameters <span class="math-tex">\(\alpha \)</span>.</p> <p>Copyright (c) - All rights reserved. Medical Image Analysis Laboratory - Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland & CIBM Center for Biomedical Imaging. 2023.</p>
Cell metadata for "The emergent landscape of the mouse gut endoderm at single-cell resolution"
<p>Cell metadata for the data published in "The emergent landscape of the mouse gut endoderm at single-cell resolution"</p> <p> </p>
Soil organic carbon and associated uncertainty at 90 m resolution for peninsular Spain
Soil organic carbon (SOC) must be quantified and monitored to assess soil management practices, adapt policies, and evaluate environmental impacts. However, due to SOC spatial variability, soil surveys become a very challenging task because of the high costs of acquiring data, operational complexity, and updating. Digital soil mapping based on machine learning approaches in combination with remote sensing techniques have enabled soil carbon spatial distribution to be significantly improved, even with limited soil samples. A legacy soil database of 8,361 georeferenced profiles and a selection of environmental data-driven covariates intimately related to soil-forming factors (e.g., biota, climate, parent material) were used to generate SOC maps. Modeling of data was based on three supervised learning approaches: quantile regression forest, ensemble machine learning and auto-machine learning. For the final SOC spatial distribution maps, each pixel was assigned the prediction from the most accurate model, i.e., lowest uncertainty. We applied this modeling technique to generate cost-effective, high-resolution maps (90 m pixel resolution) of SOC distribution, and its associated spatially explicit uncertainty, in peninsular Spain. These maps showed 15.7 g.kg-1 mean SOC concentration at 0-30 cm and 3.6 g.kg-1 at 30-100 cm depth. The total SOC stock at its effective depth was 3.8 Pg C, storing the 74% in the upper 30 cm (2.82 Pg C). The correlation between SOC observed and predictions final values showed R2=0.68 for SOCc and R2=0.54 for SOCs at the upper 30cm. The methodology proposed in this study aims to improve benchmark SOC estimates in support of the National GHG Emissions Inventory Report
High resolution stream temperature, pressure, and estimated depth from transducers in streams in the Lake Sunapee watershed, New Hampshire, USA 2010-2018
Seven in-stream HOBO pressure transducers and one reference HOBO pressure transducer have been deployed within the Lake Sunapee, NH, USA watershed. Six of the transducers have been in operation since 2010 and an additional transducer was added in 2016. The transducers record data every 15 minutes, and data are downloaded approximately three times per year (early Spring, mid Summer and late Fall). Shortly after download, the data are processed to estimate stream depth using HOBOware's Barometric Compensation Assistant and converted to a .csv file in HOBOware. The data have been QAQC'd to recode obviously errant data to NA using R programming language. No data transformation has occurred beyond basic QAQC of the data to remove known data issues and obviously errant data. The barometric pressure data from the reference transducer located on land are also included in this data package.
Advanced Resolution Canopy FLOw (ARCFLO) experiment employing the SUbcanopy Sonic Anemometer Network (SUSAN) in WS01 of the HJ Andrews Experimental Forest, July-September 2012
This dataset was collected during one of the ARCFLO (Advanced Resolution Canopy FLOw) experiment series’ field campaigns. This field campaign was carried out in WS1 of the HJ Andrews Experimental forest during July-September 2012 by the biomicrometeorology group, PI Christoph Thomas. The ARCFLO experiment series spanned a wide range of topographic conditions (flat, sloped, mountainous) and canopy architectures (grassland, orchard, open forest, dense forest) and was carried out between 2011 and 2014. It was funded through the NSF Career Award in Physical and Dynamical Meteorology to PI Christoph Thomas. The main goal of this project was to develop a novel improved framework to describe the airflow and its transport under weak-wind conditions for a continuous variation of overstory density and stratification. The objective is to i) identify forcing mechanisms of submeso motions, ii) evaluate the impact of plant canopies of different overstory density on the wind, temperature, and humidity fields, and iii) improve predictors for mixing in plant canopies that incorporate the important physical mechanisms. Observations were be made with a unique combination of new and standard techniques including optical fiber measurement of temperature structure, acoustic remote sensing, ultrasonic anemometers, and laser-illuminated flow visualizations.
Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers, or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This dataset provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) from these environments. The dataset contains 16S and 18S rRNA data from 2017, and contains 16S rRNA data for monthly (2019) and quarterly water samples (2020-ongoing). The 2017 data are published in Laas et al. 2022. A detailed list of sequence data and their accession numbers in GenBank is provided and will be updated as more data are published. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA525456 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525456) and BioProject PRJNA1018945 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1018945). This data package is associated with the following publication: Laas, P., Ugarelli, K., Travieso, R., Stumpf, S., Gaiser, E. E., Kominoski, J. S., & Stingl, U. (2022). Water column microbial communities vary along salinity gradients in the Florida Coastal Everglades wetlands. Microorganisms, 10(2), 215. https://doi.org/10.3390/microorganisms10020215 Instead of citing this package, which is an inventory, please cite the original GenBank data or journal article, as appropriate. Citation guidance for the journal article is available on the respective publisher's website.
High resolution shrub cover raster maps of the Jornada Basin LTER, including JER and CDRRC (2011)
This data package contains two raster shrub cover maps of the Jornada Experimental Range (JER) and Chihuahuan Desert Rangeland Research Center (CDRRC) in southern New Mexico, USA. The maps are derived from 1m resolution National Agriculture Imagery Program (NAIP) aerial photos acquired in 2011. A one-meter resolution raster file lists cover as non-shrub or non-shrub. A hectare resolution raster file contains fractional shrub cover values (0-1) calculated from the one-meter raster.
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.