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Labeled high-resolution orthoimagery time-series of an alluvial river corridor; Elwha River, Washington, USA.
<h2>Labeled high-resolution orthoimagery time-series of an alluvial river corridor; Elwha River, Washington, USA.</h2><h4>Daniel Buscombe, Marda Science LLC</h4><p>There are two datasets in this data release:</p><p>1. <strong>Model training dataset</strong>. A manually (or semi-manually) labeled image dataset that was used to train and evaluate a machine (deep) learning model designed to identify subaerial accumulations of large wood, alluvial sediment, water, and vegetation in orthoimagery of alluvial river corridors in forested catchments. </p><p>2. <strong>Model output dataset</strong>. A labeled image dataset that uses the aforementioned model to estimate subaerial accumulations of large wood, alluvial sediment, water, and vegetation in a larger orthoimagery dataset of alluvial river corridors in forested catchments. </p><p>All of these label data are derived from raw gridded data that originate from the U.S. Geological Survey (<i>Ritchie et al., 2018</i>). That dataset consists of 14 orthoimages of the Middle Reach (MR, in between the former Aldwell and Mills reservoirs) and 14 corresponding Lower Reach (LR, downstream of the former Mills reservoir) of the Elwha River, Washington, collected between the period 2012-04-07 and 2017-09-22. That orthoimagery was generated using SfM photogrammetry (following <i>Over et al., 2021</i>) using a photographic camera mounted to an aircraft wing. The imagery capture channel change as it evolved under a ~20 Mt sediment pulse initiated by the removal of the two dams. The two reaches are the ~8 km long Middle Reach (MR) and the lower-gradient ~7 km long Lower Reach (LR). </p><p>The orthoimagery have been labeled (pixelwise, either manually or by an automated process) according to the following classes (inter class in the label data in parentheses):</p><p>1. vegetation / other (0)</p><p>2. water (1)</p><p>3. sediment (2)</p><p>4. large wood (3)</p><h3>1. Model training dataset.</h3><p>Imagery was labeled using a combination of the open-source software Doodler (<i>Buscombe et al., 2021</i>; <a href="https://github.com/Doodleverse/dash_doodler">https://github.com/Doodleverse/dash_doodler</a>) and hand-digitization using QGIS at 1:300 scale, rasterizeing the polygons, and gridded and clipped in the same way as all other gridded data. Doodler facilitates relatively labor-free dense multiclass labeling of natural imagery, enabling relatively rapid training dataset creation. The final training dataset consists of 4382 images and corresponding labels, each 1024 x 1024 pixels and representing just over 5% of the total data set. The training data are sampled approximately equally in time and in space among both reaches. All training and validation samples purposefully included all four label classes, to avoid model training and evaluation problems associated with class imbalance (<i>Buscombe and Goldstein, 2022</i>). </p><p>Data are provided in geoTIFF format. The imagery and label grids (imagery) are reprojected to be co-located in the NAD83(2011) / UTM zone 10N projection, and to consist of 0.125 x 0.125m pixels.</p><p>Pixel-wise labels measurements such as these facilitate development and evaluation of image segmentation, image classification, object-based image-analysis (OBIA), and object-in-image detection models, and numerous potential other machine learning models for the general purposes of river corridor classification, description, enumeration, inventory, and process or state quantification. For example this dataset may serve in transfer learning contexts for application in different river or coastal environments or for different tasks or class ontologies.</p><h4>Files:</h4><p>1. Labels_used_for_model_training_Buscombe_Labeled_high_resolution_orthoimagery_time_series_of_an_alluvial_river_corridor_Elwha_River_Washington_USA.zip, 63 MB, label tiffs</p><p>2. Model_<i>training_</i> images1of4.zip, 1.5 GB, imagery tiffs</p><p>3. Model_<i>training_</i> images2of4.zip, 1.5 GB, imagery tiffs</p><p>4. Model_<i>training_</i> images3of4.zip, 1.7 GB, imagery tiffs</p><p>5. Model_<i>training_</i> images4of4.zip, 1.6 GB, imagery tiffs</p><h3>2. Model output dataset.</h3><p>Imagery was labeled using a deep-learning based semantic segmentation model (<i>Buscombe, 2023</i>) trained specifically for the task using the Segmentation Gym (<i>Buscombe and Goldstein, 2022</i>) modeling suite. We use the software package Segmentation Gym (<i>Buscombe and Goldstein, 2022</i>) to fine-tune a Segformer (<i>Xie et al., 2021</i>) deep learning model for semantic image segmentation. We take the instance (i.e. model architecture and trained weights) of the model of <i>Xie et al. (2021)</i>, itself fine-tuned on ADE20k dataset (<i>Zhou et al., 2019</i>) at resolution 512x512 pixels, and fine-tune it on our 1024x1024 pixel training data consisting of 4-class label images.</p><p>The spatial extent of the imagery in the MR is [455157.2494695878122002,5316532.9804129302501678 : 457076.1244695878122002,5323771.7304129302501678] (NAD83(2011) / UTM zone 10N). Imagery width is 15351 pixels and imagery height is 57910 pixels. The spatial extent of the imagery in the LR is [457704.9227139975992031,5326631.3750646486878395 : 459241.6727139975992031,5333311.0000646486878395] (NAD83(2011) / UTM zone 10N). Imagery width is 12294 pixels and imagery height is 53437 pixels. Data are provided in Cloud-Optimzed geoTIFF (COG) format. The imagery and label grids (imagery) are reprojected to be co-located in the NAD83(2011) / UTM zone 10N projection, and to consist of 0.125 x 0.125m pixels. All grids have been clipped to the union of extents of active channel margins during the period of interest.</p><p>Reach-wide pixel-wise measurements such as these facilitate comparison of wood and sediment storage at any scale or location. These data may be useful for studying the morphodynamics of wood-sediment interactions in other geomorphically complex channels, wood storage in channels, the role of wood in ecosystems and conservation or restoration efforts. </p><h4>Files:</h4><p>1. Elwha_MR_labels_Buscombe_Labeled_high_resolution_orthoimagery_time_series_of_an_alluvial_river_corridor_Elwha_River_Washington_USA.zip, 9.67 MB, label COGs from Elwha River Middle Reach (MR)</p><p>2. Elwha<i>MR_ imagery_ part1_ of</i>_<i> </i>2.zip, 566 MB, imagery COGs from Elwha River Middle Reach (MR)</p><p>3. Elwha<i>MR_ imagery_ part2_ of</i>_<i> </i>2.zip, 618 MB, imagery COGs from Elwha River Middle Reach (MR)</p><p>3. Elwha_LR_labels_Buscombe_Labeled_high_resolution_orthoimagery_time_series_of_an_alluvial_river_corridor_Elwha_River_Washington_USA.zip, 10.96 MB, label COGs from Elwha River Lower Reach (LR)</p><p>4. ElwhaL<i>R_ imagery_ part1_ of</i>_<i> </i>2.zip, 622 MB, imagery COGs from Elwha River Middle Reach (MR)</p><p>5. ElwhaL<i>R_ imagery_ part2_ of</i>_<i> </i>2.zip, 617 MB, imagery COGs from Elwha River Middle Reach (MR)<br> </p><p>This dataset was created using open-source tools of the Doodleverse, a software ecosystem for geoscientific image segmentation, by Daniel Buscombe (<a href="https://github.com/dbuscombe-usgs">https://github.com/dbuscombe-usgs</a>) and Evan Goldstein (<a href="https://github.com/ebgoldstein">https://github.com/ebgoldstein</a>). Thanks to the contributors of the Doodleverse!. Thanks especially Sharon Fitzpatrick (<a href="https://github.com/2320sharon">https://github.com/2320sharon</a>) and Jaycee Favela for contributing labels. </p><h3>References</h3><p>• Buscombe, D. (2023). <strong>Doodleverse/Segmentation Gym SegFormer models for 4-class (other, water, sediment, wood) segmentation of RGB aerial orthomosaic imagery (v1.0)</strong> [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.8172858">https://doi.org/10.5281/zenodo.8172858</a></p><p>• Buscombe, D., Goldstein, E. B., Sherwood, C. R., Bodine, C., Brown, J. A., Favela, J., et al. (2021).<strong> Human-in-the-loop segmentation of Earth surface imagery</strong>. Earth and Space Science, 9, e2021EA002085. <a href="https://doi.org/10.1029/2021EA002085">https://doi.org/10.1029/2021EA002085</a></p><p>• Buscombe, D., & Goldstein, E. B. (2022). <strong>A reproducible and reusable pipeline for segmentation of geoscientific imagery.</strong> Earth and Space Science, 9, e2022EA002332. <a href="https://doi.org/10.1029/2022EA002332">https://doi.org/10.1029/2022EA002332</a> See: <a href="https://github.com/Doodleverse/segmentation_gym">https://github.com/Doodleverse/segmentation_gym</a></p><p>• Over, J.R., Ritchie, A.C., Kranenburg, C.J., Brown, J.A., Buscombe, D., Noble, T., Sherwood, C.R., Warrick, J.A., and Wernette, P.A., 2021, <strong>Processing coastal imagery with Agisoft Metashape Professional Edition, version 1.6—Structure from motion workflow documentation</strong>: U.S. Geological Survey Open-File Report 2021–1039, 46 p., <a href="https://doi.org/10.3133/ofr20211039">https://doi.org/10.3133/ofr20211039</a>.</p><p>• Ritchie, A.C., Curran, C.A., Magirl, C.S., Bountry, J.A., Hilldale, R.C., Randle, T.J., and Duda, J.J., 2018, <strong>Data in support of 5-year sediment budget and morphodynamic analysis of Elwha River following dam removals</strong>: U.S. Geological Survey data release, <a href="https://doi.org/10.5066/F7PG1QWC">https://doi.org/10.5066/F7PG1QWC</a>.</p><p>• Xie, E., Wang, W., Yu, Z., Anandkumar, A., Alvarez, J.M. and Luo, P., 2021. <strong>SegFormer: Simple and efficient design for semantic segmentation with transformers</strong>. Advances in Neural Information Processing Systems, 34, pp.12077-12090.</p><p>• Zhou, B., Zhao, H., Puig, X., Xiao, T., Fidler, S., Barriuso, A. and Torralba, A., 2019. <strong>Semantic understanding of scenes through the ade20k dataset</strong>. International Journal of Computer Vision, 127, pp.302-321.</p><p><br> </p>
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>
High-resolution basin-wide correlations with dynamic time-warping: code and data for a case study from the Usseln Limestone (Late Devonian, Rhenish Massif, Germany)
<p>This dataset accompanies the manuscript of Wichern et al. (GRL, 2024), entitled "Decoding Deep-Time Rhythms: Probing the limit of Stratigraphic Correlation in the Usseln Limestone's (Late Devonian) Time-Specific Facies". It contains both datasets and code. </p> <p>The dataset concerns samples collected from the Usseln Limestone, a rock unit that underlies the Late Devonian Kellwasser Crisis deposits in the Rhenish Massif, western Germany. The data consists of high-resolution thin-section composite photos, as well as micro-XRF scanning data (both maps and depth records) for three localities. The code contains the workflow to structure and plot the micro-XRF maps and convert them to depth records, as well as the workflow to analyse these depth records using dynamic time warping. Further analytical details can be found in the supporting material of the associated manuscript.</p>
High resolution and high cadence time series of land surface categories, land use land cover, and land use land cover changes
<p>A prototype of monthly, 10 m resolution land surface categories, land use land cover (LULC) cover, and LULC change maps derived from Sentinel-2 data over three areas within Belgium, Portugal, and Sicily for the period 2018-2020. The LULC and LULC change maps were independently validated by IIASA. All products were generated within the framework of the RapidAI4EO project, funded from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101004356.</p> <p>The data description can be found below. The validation report of the LULC and LULC change maps can be found in validation_LULC.pdf and validation_change.pdf, respectively, and the validation dataset can be found in Lesiv <em>et al.</em> (2023).</p> <p><strong>Data description</strong></p> <p>Increasing the cadence of the land cover updates from the typical (multi-)annual to monthly cadence poses several challenges. First, several land cover types are difficult to discriminate without any knowledge of temporal dynamics. For instance, croplands are characterized by a dynamic of vegetation growth and a harvest period (i.e. cycles of bare soil, sparsely vegetated and vegetated periods). This contrasts with grasslands that often lack the harvest period resulting in a bare soil cover. Without this temporal information, it is difficult to distinguish a vegetated cropland field from grassland. Second, phenological changes may introduce a large intra-class variability and thus also confusion between classes. For example, the shedding of leaves during autumn or wilting of herbaceous vegetation in dry summer periods introduces spectral variability within land cover classes.</p> <p>To overcome these challenges, we developed a workflow with two main phases. The first phase aims to map land surface categories (LSC) at a monthly resolution. The next phase uses the resulting monthly LSC probability time series to classify land cover.</p> <p><strong><em>Land surface category (LSC)</em></strong></p> <p>These LSC represent basic, observable bio-geophysical properties (categories) of the Earth surface that can be predicted directly from individual monthly composites. LSC classes contain a set of vegetated and non-vegetated surface categories.</p> <p>Discrete LSC classification legend:</p> <table> <tbody> <tr> <td> <p>Map code</p> </td> <td> <p>Land cover class</p> </td> </tr> <tr> <td> <p>11</p> </td> <td> <p>Tree (leaf-on)</p> </td> </tr> <tr> <td> <p>12</p> </td> <td> <p>Shrubland (leaf-on)</p> </td> </tr> <tr> <td> <p>13</p> </td> <td> <p>Grassland</p> </td> </tr> <tr> <td> <p>14</p> </td> <td> <p>Woody vegetation (leaf-off)</p> </td> </tr> <tr> <td> <p>15</p> </td> <td> <p>Wilted herbaceous vegetation</p> </td> </tr> <tr> <td> <p>21</p> </td> <td> <p>Bare/sparse vegetation</p> </td> </tr> <tr> <td> <p>22</p> </td> <td> <p>Water</p> </td> </tr> <tr> <td> <p>24</p> </td> <td> <p>Built-up</p> </td> </tr> </tbody> </table> <p>In order to predict the LSC, we trained a CatBoost model (Dorogush et al., 2018) using a DEM, spectral bands and vegetation indices, country, the timing (month) of the spectral data, and the pseudo-probability of a U-Net model trained to segment built-up surfaces as input. Labels were derived by post-processing the land cover labels of the ESA WorldCover product (Zanaga et al., 2021). Please note that the collection of these labels was suboptimal, likely having an impact on the LULC and change maps generated in the prototype.</p> <p><strong><em>Land use land cover</em></strong></p> <p>After predicting LSC over the three AOI’s, we trained a CatBoost model using the LSC probabilities over a window of one year, country, and the timing (month) as independent variable. The use of LSC probabilities over multiple months allows to incorporate information about dynamics, which is necessary to discriminate some classes (e.g. cropland and grassland or cropland and bare). Similar to the LSC labels, the LULC labels were derived from the ESA WorldCover product v100 (year 2020), resulting in a similar legend system.</p> <p>The use of a moving window approach to predict LULC allows to (i) incorporate temporal information that is necessary to discriminate land cover classes and (ii) is expected to lead to more consistent land cover maps. It however has the disadvantage that (i) no land cover predictions are available at the beginning and the end of the time series and (ii) the timing of the predicted land cover change is not always accurate. To resolve these issues, we applied a post-processing step that compares and integrates the LULC predictions and cleaned LSC predictions.</p> <p>Discrete LC classification legend:</p> <table> <tbody> <tr> <td> <p><strong>Map code</strong></p> </td> <td> <p><strong>Land cover class</strong></p> </td> </tr> <tr> <td> <p>10</p> </td> <td> <p>Tree cover</p> </td> </tr> <tr> <td> <p>20</p> </td> <td> <p>Shrubland</p> </td> </tr> <tr> <td> <p>30</p> </td> <td> <p>Grassland</p> </td> </tr> <tr> <td> <p>40</p> </td> <td> <p>Cropland</p> </td> </tr> <tr> <td> <p>50</p> </td> <td> <p>Built-up</p> </td> </tr> <tr> <td> <p>60</p> </td> <td> <p>Bare/sparse vegetation</p> </td> </tr> <tr> <td> <p>80</p> </td> <td> <p>Permanent water bodies</p> </td> </tr> <tr> <td> <p>90</p> </td> <td> <p>Herbaceous wetland</p> </td> </tr> </tbody> </table> <p><strong><em>Land use land cover change </em></strong></p> <p>Monthly change maps were finally derived from the land cover maps. The pixel values within the change maps represent the percentage of pixels that changed with respect to the previous month over an area of 90x90m. The maps contain values between 0-100, with larger values assigned to larger change patches. A value of 100 indicates that all pixels within an area of 90x90m around the pixel were flagged as change.</p> <p><strong><em>Files</em></strong></p> <p>The zip files contain the following data:</p> <ul> <li>lsc.zip: land surface category maps over the three AOI’s</li> <li>lc.zip: LULC maps over the three AOI’s</li> <li>change.zip: change maps over the three AOI’s</li> </ul> <p>These maps are generated for each month over the period 2018-2020 for each of the tiles (see tiles.gpkg for an overview of all tiles). The files names use the following naming convention: “<em>tile</em>-<em>year</em>-<em>month</em>.tif”.</p> <p><strong><em>References</em></strong></p> <p>Myroslava Lesiv, Halyna Bun, & Martina Duerauer. (2023). Validation data set on land cover changes for RapidAI4EO project [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7825963 </p> <p>Dorogush, A. V., Ershov, V., & Gulin, A. (2018). CatBoost: gradient boosting with categorical features support. arXiv preprint arXiv:1810.11363.</p> <p><em>Zanaga, D., </em><em>et al.</em><em>., 2021. ESA WorldCover 10 m 2020 v100. </em><a href="https://doi.org/10.5281/zenodo.5571936 "><em>https://doi.org/10.5281/zenodo.5571936 </em></a></p>
Long time series (2001-2015) high-resolution crop yield and water productivity dataset of China
<p>A long-term data series, at 1-km resolution, of crop yield (kg/ha) and crop water productivity (kg/m3) for maize and wheat across China, based on the MOD16 ET product, multiple remotely sensed crop physiological and environmental indicators, and crop phenological information, using a random forest algorithm. Results showed that MOD16 products are an accurate alternative to eddy covariance flux tower data to describe crop evapotranspiration (maize and wheat RMSE: 4.42 and 3.81 mm/8d, respectively) and the proposed yield estimation model showed accuracy at local (maize and wheat rRMSE: 26.81 and 21.80%, respectively) and regional (maize and wheat rRMSE: 15.36 and 17.17%, respectively) scales. These high-resolution crop yield and CWP datasets generated in this study revealed spatiotemporal patterns of agricultural production in China and may be applied to many scenarios, including understanding effects of climate change on agricultural production capacity in China under increasing demand for food security to optimize agricultural production strategies.</p>
Ind. Ch. 60 Grant of the time of Ravivarman, seal High resolution TIFF
<p><a href="https://siddham.network/object/ob01055/">OB01055</a> Ind. Ch. 60 Grant of the time of Ravivarman, seal High resolution TIFF</p>
A high-frequency and high-resolution image time series of the Gornergletscher - Swiss Alps - derived from repeated UAV surveys
<p>This dataset is based on aerial photographs of the Gornergletscher glacial system (Switzerland) collected during ten intensive UAV surveys carried out approximately every two weeks throughout the summer 2017.</p> <p>The final products consist in a series of 10 cm resolution ortho-images, Digital Elevation Models of the glacier surface, and Matching Maps that can be used to quantify ice surface displacements.</p>
Fig. 3 in Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR)
Fig. 3. Phylogenetic tree of seven Trypanosome species and subsequent genotypes constructed with sequences of the amplicons generated by the HRMqPCR primers.
Fig. 4 in Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR)
Fig. 4. Amplification plots, melt curves and standard curves of T. copemani, T. vegrandis G7 and T. noyesi G8 prepared from a plasmid containing trypanosome species.
Fig. 5. A-D in Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR)
Fig. 5. A-D: Derivative melt curves showing mock mixed infections generated from plasmid clones containing the following DNA: (A) T. noyesi G8 and T. copemani; (B) T. vegrandis G7 and T. copemani; (C) T. vegrandis G7 and T. noyesi G8; (D) T. vegrandis G7, T. noyesi G8 and T. copemani.
Fig. 1 in Species-level identification of trypanosomes infecting Australian wildlife by High-Resolution Melting - Real Time Quantitative Polymerase Chain Reaction (HRM-qPCR)
Fig. 1. Multiple sequence alignment of a portion of the 18S rDNA of seven Trypanosome species and subsequent genotypes used to design the HRM-qPCR assays.
High-resolution wind power generation time series for Germany in the period 2000-2015
<p>High-resolution wind power generation time series for Germany in the period 2000-2015. A paper describing the applied methodology can be found in this repository as well.</p> <p>The final temporal resolution is hourly and the spatial resolution NUTS 3. The data is stored in csv and hdf5 files.</p> <p>More information on the data set, e.g. missing time stamps and versioning, can be found in readme.txt.</p>
An automatically generated high-resolution earthquake catalogue for the 2016-2017 Central Italy seismic sequence, including P and S phase arrival times
<p>Catalog of 440,697 earthquakes of the 2016-2017 Central Italy seismic sequence semi-automatically generated by Spallarossa et al. (2020). The catalogue covers one year of aftershocks following the first mainshock of the sequence (from 08242016 to 08312017).</p> <p>The catalog has been generated using the Complete Automatic Seismic Processor (CASP) procedure (Scafidi et al., 2019) to detect the events and an advanced picker engine (RSNI-Picker<sub>2</sub>; Scafidi et al., 2018; Spallarossa et al., 2014) to determine their phase arrival times. The final set of about 7 million P- and 10 million S-wave arrival times have been used to locate the events using a non-linear location algorithm (NonLinLoc; Lomax et al. 2000), with a 1D velocity model calibrated for the area (De Luca et al., 2009) and station corrections. For each event, also local magnitudes (M<sub>L</sub>) has been calculated as well as a locations quality.</p> <p>Earthquake locations quality has been classified by means of the procedure proposed by Michele et al., (2019) consisting of the combination of diverse uncertainty parameters provided by the NonLinLoc location code. Locations quality is provided in terms of a unique numeric normalized value, named quality factor, varying between qf=0 (best quality location) and qf=1 (worst quality location). Then locations have been assigned to a quality class depending on the qf parameter value according to the following scheme: A-class (0 < qf ≤ 0.25), B-class (0.25 < qf ≤ 0.50), C-class (0.50 < qf ≤ 0.75), and D-class (0.75 < qf < 1.00). The earthquake locations are distributed between the quality classes as A-30.6%, B-31.4%, C-18.6%, and D-19.4% (details in Spallarossa et al., 2020).</p> <p>We accompanied the catalogue with the 30 events with M>3.5 missed by our procedure (bring the total number of events to 440,727), including the first Amatrice mainshock (M<sub>W</sub>6.0; see Spallarossa et al., 2020). These 30 missing events recognisable by the ID starting with ISI), have been taken from INGV bulletin (<a href="http://terremoti.ingv.it">http://terremoti.ingv.it</a>; ISIDe Working Group., 2007), manually generated. These additional events report INGV locations and magnitude parameters while are missing related quality factors and quality class, being generated by a different procedure.</p> <p>We added to the larger events, the available moment magnitudes (M<sub>W</sub>) from Time Domain Moment Tensor catalogue (<a href="http://terremoti.ingv.it/tdmt">http://terremoti.ingv.it/tdmt</a>; Scognamiglio et al., 2006).</p> <p>The catalog is in csv format, semicolon separator, ordered by origin time and the header content is the following:</p> <ul> <li>Id-event – ID</li> <li>Latitude (°) expressed in decimal degrees - LAT</li> <li>Longitude (°) expressed in decimal degrees - LON</li> <li>Depth(km) hypocentral depth expressed in kilometres - DEP</li> <li>Year of origin time in the format yyyy - YR</li> <li>Month of origin time in the format mo - MON</li> <li>Day of origin time in the format dd - DY</li> <li>Hour of origin time in the format hh - HR</li> <li>Minute of origin time in the format mi - MIN</li> <li>Second of origin time in the format XX.XXX s - SEC</li> <li>Local Magnitude - ML</li> <li>Standard deviation of the Local Magnitude – STD</li> <li>Moment Magnitude – Mw (from TDMT)</li> <li>Horizontal Error (from NLL output) (km) expressed in kilometres - ERH</li> <li>Vertical Error (from NLL output) (km) expressed in kilometres - ERZ</li> <li>RMS (from NLL output) (s) expressed in seconds - RMS</li> <li>Number of Phases – NPHS</li> <li>Stations Azimuthal GAP (°) expressed in decimal degrees - GAP</li> <li>Quality factor - Qf</li> <li>Quality class - Qc</li> </ul> <p> </p> <p>De Luca G., M. Cattaneo, G. Monachesi and A, Amato (2009). Seismicity in the Umbria-Marche region from the integration of national and regional seismic networks. Tectonophysics, 476(1), 219-231. doi: 10.1016/j.tecto.2008.11.032.</p> <p>ISIDe Working Group. (2007). Italian Seismological Instrumental and Parametric Database (ISIDe). Istituto Nazionale di Geofisica e Vulcanologia (INGV); https://doi.org/10.13127/ISIDE.</p> <p>Lomax, A., J. Virieux, P. Volant, and C. Berge-Thierry (2000). Probabilistic earthquake location in 3D and layered models: introduction of a Metropolis–Gibbs method and comparison with linear locations. In: Advances in seismic event location, ed. C. H. Thurber and N. Rabinowitz, 101–134. Dordrecht and Boston: Kluwer Academic Publishers.</p> <p>Michele, M., Latorre, D., Emolo, A. (2019). An Empirical Formula to Classify the Quality of Earthquake Locations. Bulletin of the Seismological Society of America. Vol. 109, No. 6, pp. 2755–2761, December 2019, doi: 10.1785/0120190144.</p> <p>Scafidi, D., Viganò A., Ferretti G., and Spallarossa D. (2018). Robust picking and accurate location with RSNI-Picker2: real-time automatic monitoring of earthquakes and non-tectonic events, Seismol. Res. Lett, Vol. 89 (4), pp. 1478-1487, doi: 10.1785/0220170206.</p> <p>Scafidi D, Spallarossa D, Ferretti G, Barani S, Castello B, Margheriti L (2019). A complete automatic procedure to compile reliable seismic catalogs and travel-time and strong-motion parameters datasets. Seismol Res Lett 90(3):1308–1317.</p> <p>Scognamiglio, L., Tinti, E., Quintiliani, M. (2006). Time Domain Moment Tensor [Data set]. Istituto Nazionale di Geofisica e Vulcanologia (INGV). https://doi.org/10.13127/TDMT.</p> <p>Spallarossa, D., G. Ferretti, D. Scafidi, C. Turino, and M. Pasta (2014). Performance of the RSNI-Picker, Seismol. Res. Lett. 85, 1243–1254.</p> <p>Spallarossa D., Cattaneo M., Scafidi D., Michele M., Chiaraluce L., Segou M. and I. G. Main (2020). An automatically generated high-resolution earthquake catalogue for the 2016-2017 Central Italy seismic sequence, including P and S phase arrival times. Geophys. J. Int. doi: 10.1093/gji/ggaa604.</p>
High-Resolution Beach Profile Time Series: Morecambe Bay, 2007-2022
<p><strong>Description:</strong> This dataset provides a comprehensive collection of beach profile measurements for Morecambe Bay, covering a 16-year period from 2007 to 2022. The data was collected and shared by Sefton Council (Sefton MBC), UK, as part of the coastal monitoring programme. Captured biannually during spring and autumn, the data offers valuable insights into the bay's coastal morphology and dynamics.</p> <p><strong>Data Description:</strong></p> <ul> <li><strong>Beach Transects:</strong> Detailed profiles are provided for various locations along the Morecambe Bay coastline. Station numbers are used to identify each measurement point on a dedicated map (included within the data).</li> <li><strong>Temporal Coverage:</strong> The dataset encompasses measurements conducted biannually, capturing seasonal variations in beach profiles.</li> </ul>
SESMG scenario-files of the study "Model-based run-time and memory reduction for a mixed-use multi-energy system model with high spatial resolution"
<p>This dataset contains model scenario-files belonging to the publication "Model-based run-time and memory reduction for a mixed-use multi-energy system model with high spatial resolution".</p> <p>The individual scenarios can be executed and evaluated with the "Spreadsheet Energy System Model Generator" (<a href="https://github.com/chrklemm/SESMG">SESMG</a>) <a href="https://github.com/chrklemm/SESMG/tree/v0.4.0rc1">v0.4.0rc1</a></p> <p>The respective file names indicate to which model run mentioned in the main study the scenario-files belong. For model runs for which no sepparate scenario file exists, the scenario "reference.xlsx" with adjusted SESMG settings was used.</p> <p> </p>
Multi-year high time resolution measurements of fine PM at 13 sites of the French Operational Network (CARA program)
<p>These datasets correspond to long-term measurements of atmospheric aerosol components from Aerosol Chemical Speciation Monitor (ACSM) and multi-wavelength Aethalometer (AE33) instruments collected between 2015 and 2021 at 13 (sub)urban sites as part of the French CARA program. </p> <p>The datasets contain the mass concentrations of major chemical species within PM1, namely organic aerosols (OA), nitrate (NO3-), ammonium (NH4+), sulfate (SO42-), non-sea-salt chloride (Cl-), and equivalent black carbon (eBC). </p> <p>Rigorous quality control, technical validation, and environmental evaluation processes were applied, adhering to both the guidance from the French reference laboratory for air quality monitoring and the Aerosol, Clouds, and Trace gases Research Infrastructure (ACTRIS) standard operating procedures.</p> <p>These data are discussed in an article in submission, please cite it when using the data.</p>
A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia
<p>This repository hosts the raw data and source code for the paper entitled " A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia" [DOI: 10.7717/peerj.10106].</p> <p>Two zip archives are available:</p> <p>Raw data and methods evaluation.zip - Retains empirical data and method evaluation code (R scripts) that relate to data presented in the results and discussion sections of the article, specifically, Figures 3 -11 and Tables 1 and 2.</p> <p>RTmap_source_code_and_data_structure.zip - This repository hosts the source code for <a href="http://austemperature.live/">http://austemperature.live/</a>, as described in the methods section of the article. A README.docx presents the contents and subsequent procedures for deploying the mapping code and web map application.</p> <p>For further information about this files please email:</p> <p>mweb7041@uni.sydney.edu.au</p> <p> </p>
High-resolution wall-to-wall time series predictions of seasonal maize area and yield for Rwanda over 2019-2023
<p>This is the companion dataset to publication {TBD}. It contains 1) seasonal composites of predicted maize cover and yield at 10 m resolution in Rwanda for two annual agricultural seasons over five years, 2) scripts for the end-to-end machine learning pipeline that produces these data products, and 3) data or references needed as inputs to the pipeline. </p> <h2>1) Maize cover and yield seasonal composites</h2> <p>The data are provided here as netCDF4 files with four dimensions for x, y, band, and season. They can also be accessed as Google Earth ImageCollections at: </p> <ul> <li>https://code.earthengine.google.com/?asset=projects/b2p-geospatial/assets/lulc_classifier_composite</li> <li>https://code.earthengine.google.com/?asset=projects/b2p-geospatial/assets/maize_yield_composite </li> </ul> <h3>Land cover and maize classification</h3> <p>The land cover classification file is found at <code>data/composites/lulc_classifier_Rwanda_2019to2023.nc</code>.</p> <p>The land cover classification images contain 3 bands/variables: <em>maizeProb</em>, the raw predicted probability of the pixel being maize given by the gradient boosted tree model; <em>majorityClass</em>, the categorical land cover class with the highest predicted probability among any of the nine classes in the respective pixel; and <em>optimalClass</em>, the categorical land cover class adjusted to agree with national statistics for expected maize area.</p> <p>The land cover classes map to the raster values as follows: </p> <div> <div> <pre>{<br> 1: 'maize',<br> 2: 'nonmaize_annual',<br> 3: 'nonmaize_perennial',<br> 4: 'scrub_shrub_land',<br> 5: 'forest',<br> 6: 'flooded_vegetation',<br> 7: 'water',<br> 8: 'structure',<br> 9: 'bare'<br>}</pre> </div> </div> <p>The dataset includes 5 years (2019-2023) and 10 seasons - the available time period at time of publication. In Rwanda, maize is typically planted and harvested during two distinct agricultural seasons per year: Season A from September to February and Season B from March to June. Therefore the seasons in the data are: 2019_Season_A, 2019_Season_B, 2020_Season_A, 2020_Season_B, 2021_Season_A, 2021_Season_B, 2022_Season_A, 2022_Season_B, 2023_Season_A, 2023_Season_B.</p> <h3>Maize yield</h3> <p>The maize yield file is found at <code>data/composites/maize_yield_Rwanda_2019to2023.nc</code>.</p> <p>Each of the images in the yield composites has 3 bands/variables also: <em>maizeYield</em>, the model's output of continuous predicted yield (kg/ha) in each pixel regardless of land class; <em>maizeYield_majorityClass</em>, predicted maize yield masked to the majority class land classification; and <em>maizeYieldAdj_optimalClass</em>, where the raw predicted yields were masked to the optimal maize classification land cover layer and normalized to national statistics. </p> <p>The dataset includes the same seasons as the classification product; see above for a description.</p> <h2>2) End-to-end machine learning pipeline</h2> <p>All earth observation imagery, analysis, and outputs unless otherwise stated were hosted in the Google Earth Engine (GEE) environment and developed with the Earth Engine Python API in Python v3.10. To set up a local conda environment use the <code>scripts/environment.yml</code> file. The user must have <a href="https://cloud.google.com/storage">Google Cloud Storage (GCS)</a> and <a href="https://cloud.google.com/earth-engine">Google Earth Engine (GEE)</a> accounts. The pipeline, at this scale, will incur some processing and storage fees, although Google offers a free trial to all new users and the total cost of the high-resolution wall-to-wall predictions is nominal (~$20 for one season). </p> <p>The scripts needed to perform the pipeline are located in the <code>scripts</code> folder. </p> <p>The files contained in the <code>scripts/helpers</code> directory will be called by various subsequent scripts and do not to be run interactively by the user. </p> <p>Follow the script in the order described below. The user should pause after running each script and confirm that all outputs were created and loaded to GCS before continuing the pipeline; for some steps this may take hours to days depending on processing speed. </p> <h3>Google Cloud Storage and Earth Engine set-up</h3> <p>Users should specify the names of the bucket and asset project that were chosen during set up of their GCS and GEE environments in the <em>Objects</em> section of <code>scripts/helpers/maize_pipeline_0_workspace.py</code>.</p> <h3>Pipeline set-up</h3> <p>In <code>scripts/pipeline_setup</code>, you will find the following scripts to perform data preparation of inputs into model building and prediction. </p> <ul> <li><code>maize_pipeline_1_clean_training_data.py</code> - Cleans and merges all available crop label and yield data for model training and validation</li> <li><code>maize_pipeline_2_dwnld_data_training.py</code> - Downloads satellite-derived and auxiliary features at training data points for model building</li> <li><code>maize_pipeline_3_dwnld_data_inference.py</code> - Downloads satellite-derived and auxiliary features at every 10 m pixel in Rwanda on a district-wise basis for prediction</li> </ul> <h3>Land cover and maize classification</h3> <p>In <code>scripts/maize_classification</code>, you will find the following scripts to perform model building, prediction, and post-processing for the classificaton of land cover type and maize cover.</p> <ul> <li><code>maize_classifier_1_feature_selection.py</code> - Selects features subset for land cover classification with mutual information score or variable importance</li> <li><code>maize_classifier_2_build_model.py</code> - Builds gradient boosted tree model for land cover classification from training data</li> <li><code>maize_classifier_3_prediction.py</code> - Applies model for land cover classification to every 10 m pixel in Rwanda by season and district</li> <li><code>maize_classifier_4_postprocess.py</code> - Mosaics district-wise predictions and normalizes maize cover predictions to national agricultural statistics</li> </ul> <h3>Maize yield</h3> <p>In <code>scripts/maize_yield</code>, you will find the following scripts to perform modeling building, prediction, and post-processing for maize yield estimation. </p> <ul> <li><code>maize_yield_1_build_model.py</code> - Builds gradient boosted tree model and performs bias correction for maize yield estimation from training data</li> <li><code>maize_yield_2_prediction.py</code> - Applies model for maize yield estimation to every 10 m pixel in Rwanda by season and district</li> <li><code>maize_yield_3_postprocess.py</code> - Mosaics district-wise predictions and normalizes maize yield predictions to national agricultural statistics</li> </ul> <p>If you are running the entire pipeline with refreshed training data and model building, run each of these scripts, in order. By default, the script will run all A and B seasons from 2019A to current. Otherwise, if you just wish to re-run or update seasonal predictions from the existing classification or yield model run <code>maize_pipeline_3_dwnld_data_inference.py</code> to download the seasonal feature data across Rwanda and <code>maize_classifier_3_prediction.py</code>and <code>maize_classifier_4_postprocess.py</code> for classification predictions or <code>maize_yield_2_prediction.py</code> and <code>maize_yield_3_postprocess.py</code> for yield predictions, making sure to specify which season(s) are of interest in each script. However to do this, you also need to have a copy of the previously built models in your GCS (provided at <code>data/models</code>). </p> <h2>3) Input data into machine learning pipeline</h2> <p>A description of datasets that must be sourced outside of the GEE platform is provided below. When available, the primary data source is also included in the directory <code>data/baselayers</code>. All other data, including Sentinel-2 imagery, auxiliary data, and other existing global land cover classificaiton products are hosted on GEE and called by the scripts directly. All datasets last accessed on 12 March 2024.</p> <h3>Administrative and geological boundaries</h3> <ul> <li>World Countries - Downloaded from <a href="https://datacatalog.worldbank.org/search/dataset/0038272/World-Bank-Official-Boundaries">The World Bank Official Boundaries</a> and included here at <code>data/baselayers/World_Countries</code>.</li> <li>Rwanda district boundaries - Downloaded from <a href="https://datacatalog.worldbank.org/search/dataset/0041453/Rwanda-Admin-Boundaries-and-Villages">The World Bank Rwanda Admin Boundaries And Villages</a> and included here at <code>data/baselayers/WB_NISR_2018</code>. This should be loaded into a FeatureCollection GEE asset named <em>districts_fc</em> for use in the pipeline. </li> <li>Rwanda agro-ecological zones - Downloaded from <a href="https://doi.org/10.1371/journal.pone.0149239">Nzeyimana, Hartemink & Geissen (2016)</a> and included here at <code>data/baselayers/MINAGRI_AEZ_1980</code>. This should be loaded into a FeatureCollection GEE asset named <em>aez_rwanda</em> for use in the pipeline. </li> </ul> <h3>Global land cover classification product</h3> <ul> <li>Microsoft/Impact Observatory LULC - Although the <a href="https://planetarycomputer.microsoft.com/dataset/io-lulc-9-class">10m Annual Land Use Land Cover (9-class) V1</a> product contains data from 2017-2022, only the LULC map from the year 2021 was used, provided here at <code>data/baselayers/impactobs_lulc_rwa_2021.tif</code>. This should be loaded into an ImageCollection GEE asset named <em>impact_obs_lulc</em> for use in the pipeline.</li> </ul> <p>(The others - Dynamic World and ESA's WorldCover - are hosted on GEE directly.)</p> <h3>Land cover labels and maize yield crop cuttings</h3> <ul> <li>One Acre Fund - Contact authors to request access as this dataset is not hosted publicly. </li> <li>RTI International - The original source of this data (Radiant MLHub) has been discontinued, but users may be able to access it via <a href="https://beta.source.coop/repositories/rti/rwanda-crop-type/">Source Cooperative</a>. The data is also included here at <code>data/baselayers/rti_rwanda_crop_type_labels</code>. </li> <li>Crop Harvest - Downloaded from <a href="../records/7257688">Tseng et al. (2021, v13)</a> and included here at <code>data/baselayers/CropHarvest</code>. These data points were ultimately not used in the training data, but are provided here for others that may find this dataset useful in their context.</li> </ul> <h3>Rwanda national agricultural surveys</h3> <ul> <li>National Institute of Statisitcs Rwanda (NISR) - Downloaded from <a href="https://statistics.gov.rw/datasource/seasonal-agricultural-survey">NISR Seasonal Agricultural Survey</a> and existing seasons included here at <code>data/baselayers/NISR_Seasonal_Ag_Surveys</code>. For each subsequent season, the user will have to download the spreadsheet of survey results from the NISR webpage (linked) and add the respective season to the <code>get_nisr_data</code> function in the <code>helpers/maize_pipeline_0_helpers_postprocess.py</code> script to clean and read in the data for use in the pipeline. </li> </ul> <p> </p>
High time resolution search for prompt radio emission from the long GRB 210419A with the Murchison Widefield Array
<p>The time series of Stokes parameters in the PSRFITS format formed from the MWA data at the position of GRB 210419A.</p>
Data from: Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
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.