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1,255 results for “high-resolution”
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Ramped Pyrolysis Oxidation (RPO) coupled radiocarbon (14C-DOC) and stable carbon (13C-DOC), high-resolution molecular composition (FT-ICR MS), and biodegradable dissolved organic carbon (BDOC) of groundwater, river water, and lagoon water in northeast Alaska, 2017
Supra-permafrost groundwater (SPGW), river water, and lagoon water were sampled near Kaktovik, AK to assess the reactivity and origin of dissolved organic matter (DOM) across interconnected hydrologic systems during late summer. Water samples were collected on August 17th 2017 from SPGW along the beach of Jago Lagoon (Jago GW), surface water from the Jago River’s main channel above tidal influence (Jago R), and from the water column of Kaktovik Lagoon at 2–3 m depth (KA LW). Measurements were made from grab samples for river and lagoon water, and from a composite sample for SPGW gathered from 10 individual shoreline locations. Data include dissolved organic carbon concentration (DOC, mg C L-1), Ramped Pyrolysis Oxidation (RPO) derived fraction compositions of 13C-DOC (δ13C ‰), 14C-DOC (in fraction modern), and method/instrumental error in the 14C and 13C results, and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) molecular composition and summarized compound classes. Biodegradable DOC (BDOC) bottle experiments were performed using all three sample types, where DOC concentration was subsequently measured at 2, 7, 14, and 28 days. FT-ICR MS composition was subsequently measured at the 28-day timepoint to track changes in molecular formulae and compound class relative abundance following biodegradation. Data from RPO serial thermal oxidation include temperature and normalized CO2 profiles for each background sample. Thermal-oxidation profiles of CO2 were transformed into non-parametric activation energy (E) distributions using an inverse model. Model output includes C mass of oxidized CO2 (µg C), Tmax (K), Emax (kJ mol-1), Emean (kJ mol-1), Estd (kJ mol-1), and p(0,E)max of user-defined sample fractions. FT-ICR MS results include a summary table of the relative abundance of compound classes (e.g., unsaturated phenolic, polyphenolic, aliphatic, condensed aromatics, peptide-like) and elemental groupings (e.g., CHO-type, CHON-type, CHOS-type, CHON
Cascade project at North Temperate Lakes LTER - High-resolution spatial analysis of CASCADE lakes during experimental nutrient enrichment 2015 - 2016
This dataset contains high-resolution spatio-temporal water quality data from two experimental lakes during a whole-ecosystem experiment. Through gradual nutrient addition, we induced a cyanobacteria bloom in an experimental lake (Peter Lake) while leaving a nearby reference lake (Paul Lake) as a control. Peter and Paul Lakes (Gogebic county, MI USA), were sampled using the FLAMe platform (Crawford et al. 2015) multiple times during the summers of 2015 and 2016. In 2015 nutrient additions to Peter Lake began on 1 June, and ceased on 29 June, Paul Lake was left unmanipulated. In 2016 no nutrients were added to either lake. Measurements were taken using a YSI EXO2 probe and a Garmin echoMap 50s. Sensor- data were collected continuously at 1 Hz and linked via timestamp to create spatially explicit data for each lake. Crawford, J. T., L. C. Loken, N. J. Casson, C. Smith, A. G. Stone, and L. A. Winslow. 2015. High-speed limnology: Using advanced sensors to investigate spatial variability in biogeochemistry and hydrology. Environmental Science & Technology 49:442–450.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Cascade Project at North Temperate Lakes LTER – High-resolution Spatial Data for Whole Lake Experiments 2018 - 2019
Spatial measurements of water quality from Peter and Paul lakes in 2018 and 2019. In 2019, inorganic nitrogen and phosphorus were added to Peter Lake daily to cause an algal bloom while Paul Lake was an unmanipulated reference lake. In 2018, both lakes were sampled 1 time per week, while in 2019 lakes were sampled three times per week. Measurements were taken using the FLAMe sampling platform (Crawford et al. 2015, Environmental Science and Technology 49:442-450), which was driven in a grid pattern and recorded GPS coordinates and water measurements at 1Hz to create high resolution spatial maps.
Mediterranean Cyclone tracks between 1979-2018 (40 years) from a high-resolution perspective using ECMWF ERA5 dataset
<p>The present dataset presents the trajectories of the 13,157 cyclones identified within the Mediterranean Region (MR) between 1979 and 2018 (40 years). These cyclone tracks were obtained using the new Cyclone Detection and Tracking Method (CDTM) described in Aragão e Porcù (2021) to take advantage of the recent availability of a high-resolution reanalysis dataset of ECMWF ERA5. The CDTM uses hourly data of Geopotential Height at 1000 hPa with a spatial resolution of 0.25°x0.25°, and the analysis' domain covers the area within 15°W to 48° E and 21° N to 54°N. Additionally, trying to eliminate artificial low-pressure cores, short-living thermal-lows or too weak cyclones as much as possible, the present study only considered cyclones lasting more than 24h.<br> The dataset presents hourly information for all cyclones from the cyclogenesis time to the cyclolysis time. Each record presents: [1] Cyclone ID (integer, 8 digits), [2] Cyclone centre longitude position (°E, real, 8 digits, 3 decimal digits), [3] Cyclone centre latitude position (°N, real, 8 digits, 3 decimal digits), [4] Year (integer, 4 digits), [5] Month (integer, 2 digits), [6] Day (integer, 2 digits), [7] Hour (integer, 2 digits), [9] Cyclone centre Geopotential Height at 1000 hPa (m, real, 9 digits, 3 decimal digits).<br> The analyses presented in Aragão e Porcù (2021) revealed that the proposed CDTM is capable to capture almost the totality of the observed cyclones, as well as describing its respective area of cyclogenesis, trajectories, and durations. More than an adaptation to a high-resolution dataset, the method brings as its primary contribution a suitable set of parameters to systematically identify and track the cyclonic activities in the Mediterranean, where cyclones do not have sizeable horizontal pressure gradients and present a shorter lifetime compared to open-ocean cyclones.</p> <p>Cite this article</p> <p>Aragão, L., Porcù, F. Cyclonic activity in the Mediterranean region from a high-resolution perspective using ECMWF ERA5 dataset. <em>Clim Dyn</em> (2021). https://doi.org/10.1007/s00382-021-05963-x</p>
Extended data for the paper: "SentemQC - A novel and cost-efficient method for quality assurance and quality control of high-resolution frequency sensor data in fresh waters"
<p>Extended data 1 to 4 for the software article:<br>SentemQC - A novel and cost-efficient method for quality assurance and quality control of high-resolution frequency sensor data in fresh waters. </p> <p>The extended data is tables and a Figure output and input from/to SentemQC runs relevant for the SentemQC paper.</p>
High-resolution orthoimagery of the Altamaha River estuary in November 2017 and October 2018
We acquired two high-resolution (0.15-m per pixel) color digital images of the salinity gradient of the Altamaha River estuary in November 2017 (1 month after Hurricane Irma) and October 2018. Flights ranged from the mouth of the estuary all the way up to the tidal fresh forest habitat. The 1:1200 scale orthoimagery is comprised of 4-bands (Red, Green, Blue, Near Infrarad (RGBNIR)) collected with a Ground Sample Distance (GSD) of 0.5 foot using a Leica ADS100 airborne digital sensor. Individual tiles were georectified using ground control points and merged into a domain-wide mosaic.
Effects of Phase Regression on High-Resolution Functional MRI of the Primary Visual Cortex
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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>
Wollestraat 29, Bruges (BE): high-resolution images of dry wood cores taken form a medieval floor joists, for tree-ring analysis
<ul><li>Dry-wood cores taken from historical timbers of a floor joists in the medieval building 'De Oude Steen', Wollestraat 29, Bruges (Belgium).</li><li><a href="https://id.erfgoed.net/erfgoedobjecten/29956 ">https://id.erfgoed.net/erfgoedobjecten/29956 </a></li><li>The cores were sampled at 22/02/2023 with a dry-wood borer (internal diameter 12 mm, external diameter 19 mm).</li><li>The cores were surfaced with increasingly finer sanding papers, from P60 up to P4000.</li><li>The cores were photograpphed with a Sony alpha7R IV full frame camera and FE 90 mm F/2.8G macro lens.</li><li>The<a href="https://www.wsl.ch/en/services-produkte/skippy/"> Skippy</a> system served as the image capturing platform.</li><li>The individual digital macro-photos were stitched with PTGui into a mosaic image (.tiff).</li><li>The mosaic images have a resolution of ~4 µm.</li></ul>
A Missing Piece of the E-Region Puzzle: High-Resolution Photoionization Cross Sections and Solar Irradiances in Models
<p>Dataset corresponding to the associated publication, "A Missing Piece of the E-Region Puzzle: High-Resolution Photoionization Cross Sections and Solar Irradiances in Models." The dataset includes high-resolution photoionization and photoabsorption cross section for O and N<sub>2</sub> as well as high-resolution solar spectrum. Photoionization rates from model runs obtained from AURIC and the Meier photoionization code are also included. Please refer to the readme for information on the data structure.</p> <p><strong>***Please note that the paper is under review and has not been accepted yet.***</strong></p>
A Danish high-resolution dataset for six office rooms with occupancy, indoor environment , heating, ventilation, lighting and room control monitoring
<p>A dataset containing measurement data for six office rooms in Aalborg Denmark.<br>All the measurements have been resampled to 5 minute resolution<br>The measurements consists of:</p> <ul> <li>BMS data for the rooms</li> <li>Occupancy for the rooms (from cameras)</li> <li>BMS data for the AHU supplying the rooms</li> <li>BMS data for the Heating system supplying the rooms</li> </ul> <p>Changes from v2<br>It was found that the pressure difference measurements across the exhaust fan was faulty and the following variables have therefore been removed:</p> <ul> <li>Ventilation:Fan__air_flow__exhaust</li> <li>Ventilation:Fan__pressure_difference__exhaust</li> </ul> <p>More data has been added, now increasing the dataset to span the rest of 2023. To better handle the changes between standard time and daylight-saving time the column named "timestamp" has been adjusted so the datetime format now follows the ISO 8601 format YYYY-MM-DDThh:mm:ss+hhmm. the +hhmm changes between 0100 (Danish standard time) and 0200 (Danish daylight-saving time).</p> <p> </p>
High-resolution images from a low-cost imaging device for hyphae in soil
<p>This dataset contains high-resolution images produced by a low-cost imaging device for hyphae in soil called <em>Hyphascope</em>. Using a digital microscope camera (DMC; 600× magnification),<em> </em>the device takes detailed images (0.83 × 0.62 mm imaged area) of a soil profile from evenly spaced camera positions within a user-defined volume. Repeated imaging of a soil profile with <em>Hyphascope</em> enables researchers to observe and quantify changes in the amount, distribution, and morphology of hyphae.</p> <p>Individual images were combined using the <em>Grid/Collection stitching</em> plugin of the <em>Fiji</em> distribution of <em>imageJ</em> (Preibisch et al. 2009). All images are supplied in the JPG format to limit their file size. For more details on the assembly and application of <em>Hyphascope</em>, see <a href="https://doi.org/10.17504/protocols.io.bp2l6xo3zlqe/v1">this protocol on protocols.io</a>. For information on the development, limitations, and expected outcomes of the protocol, see <a href="https://doi.org/10.1371/journal.pone.0318083">this article</a> published in PLOS ONE. </p> <p> </p> <div> <h2>Image set 1: 10 × 10 mm soil profile area at 20 - 30 mm soil depth</h2> <p>Imaged at 0.65 μm px<sup>-1</sup> (39200 dpi)* in a <em>Quercus serrata</em> grove on 2023/05/25 during a period of high hyphal density in the soil.</p> <h3>Individual images (18 rows × 14 images each)</h3> <ul> <li> <p><em>set1_foc00000.zip</em> (focus depth 0 mm)</p> </li> </ul> <h3>Combined images</h3> <ul> <li> <p><em>set1_foc00000_combined.jpg</em> (focus depth 0 mm)</p> </li> </ul> <h2>Image set 2: 5 × 5 mm soil profile area at 100 - 105 mm soil depth</h2> <p>Imaged at 0.52 μm px<sup>-1</sup> (49000 dpi) in a <em>Quercus serrata</em> grove on 2023/09/25.</p> <h3>Individual images (9 rows × 7 images each)</h3> <ul> <li> <p><em>set1_foc00000.zip</em> (focus depth 0 mm)<em><br></em></p> </li> <li> <p><em>set1_foc00025zip</em> (focus depth 0.025 mm)</p> </li> <li><em>set1_foc00050.zip</em> (focus depth 0.05 mm)</li> </ul> <h3>Combined images</h3> <ul> <li> <p><em>set1_foc00000_combined.jpg</em> (focus depth 0 mm)</p> </li> <li> <p><em>set1_foc00025_combined.jpg</em> (focus depth 0.025 mm)</p> </li> <li><em>set1_foc00050_combined.jpg</em> (focus depth 0.05 mm)</li> </ul> <h2>Image set 3: 5 × 5 mm soil profile area at soil surface level</h2> <p>Imaged at 0.52 μm px<sup>-1</sup> (49000 dpi) in a <em>Quercus serrata</em> grove on 2023/10/14 during a rain event.</p> <h3>Individual images (9 rows × 7 images each)</h3> <ul> <li> <p><em>set2_foc00000.zip</em> (focus depth 0 mm)<em><br></em></p> </li> <li> <p><em>set2_foc00025zip</em> (focus depth 0.025 mm)</p> </li> <li><em>set2_foc00050.zip</em> (focus depth 0.05 mm)</li> </ul> <h3>Combined images</h3> <ul> <li> <p><em>set2_foc00000_combined.jpg</em> (focus depth 0 mm)</p> </li> <li> <p><em>set2_foc00025_combined.jpg</em> (focus depth 0.025 mm)</p> </li> <li><em>set2_foc00050_combined.jpg</em> (focus depth 0.05 mm)</li> </ul> <p> </p> <p> </p> <p><em>*Units of imaging resolution: </em></p> <ol> <li><em>pixel width (μm px-1), i.e. the horizontal or vertical distance on the imaged surface covered by a single pixel; </em></li> <li><em>dots per inch (dpi), i.e. the number of pixels along a horizontal or vertical distance of 25.4 mm on the imaged surface.</em></li> </ol> </div>
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
<p><em>Aspergillus fumigatus </em>is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on <em>de novo</em> assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in <em>A. fumigatus</em>. We provide evidence for three distinct populations of <em>A. fumigatus</em>, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, <em>A. fumigatus</em> demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.</p> <p>Accompanying manuscript is available as preprint at <a href="https://dx.doi.org/10.1101/2021.12.12.472145">https://dx.doi.org/10.1101/2021.12.12.472145</a> </p> <p>Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of <em>Aspergillus fumigatus</em> Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145</p>
The potential of low-cost UAVs and open-source photogrammetry software for high-resolution monitoring of alpine glaciers: A case study from the Kanderfirn (Swiss Alps)
<p>This dataset contains high-resolution orthophotos (5 x 5 cm) and digital surface models (25 x 25 cm) of the Kandernfirn Glacier located in the Swiss Alps. Aerial images were aquired with a self-developed fixed-wing Unmanned Aerial Vehicle during ten surveys on five different days in 2017 and 2018. The open-source photogrammetry software OpenDroneMap (version 0.4.1) was used for image processing.</p> <p>The orthophotos and digital surface models were validated through dGNSS point measurements of ground control points. Please refer to the corresponding paper for information on the horizontal and vertical accuracy of the files.</p>
A high-resolution, multi-decadal, free-running, hydrodynamic simulation of the East Australia Current System using the Regional Ocean Modeling System (Version 3.0, 1994-2019)
<p>The data is from a Regional Ocean Modelling System free-running, hydrodynamic simulation of the East Australian Current System. The model has a horizontal resolution of 2.5-6 km in the cross-shore direction and 5 km in the alongshore direction, and 30 vertical s-levels. The model domain covers the southeastern Australia oceanic region from 25.1-41.5°S and 147.1-162.2°E, and the grid is orientated 20 degrees clockwise to be predominantly orientated alongshore. The time period covered is 02 Jan 1994 to 28 Feb 2019. The model outputs provided are daily averages of the following variables: Two-dimensional variables: Sea surface height (zeta), barotropic cross-grid velocity (u) and barotropic along-grid velocity (v). Three-dimensional variables: Temperature (temp), salinity (salt), density (rho), cross-grid velocity (u), along-grid velocity (v) and vertical velocity (w), temperature time rate of change (temp_rate), temperature horizontal advection term (temp_hadv), temperature vertical advection term (temp_vadv), temperature horizontal diffusion term (temp_hdiff), temperature vertical diffusion term (temp_vdiff). In this version, the heat budget terms (temp_rate, temp_hadv, temp_vadv, temp_hdiff and temp_vdiff) are set to be zeros on the land.</p> <p> </p> <p>This model is part of the <a href="../records/8294716"><strong>South East Australian Coastal Ocean Forecast System (SEA-COFS)</strong></a> suite of models.</p>
A high-resolution 4D geospatial laser scan dataset of the beach at Mariakerke Bad, Belgium
<p>This dataset contains a high resolution (in both time and space) laser scan data set of a 1-year measurement campaign in 2017 and 2018 in the seaside resort of Mariakerke Bad in Belgium. The measurements consist of 8417 hourly laserscans of a 400 meter stretch of beach. The measurement campained was performed to study variations in shoreward sand transport at urbanized beaches. </p> <p>Laserscan data is stored in local coordinates. Time dependent corrections per laserscan epoch are provided next to a global transformation matrix to transform the local coordinates to the Belgium Lambert 2008 coordinate system.</p> <p>This data is provided as is and is licensed under the Creative Commons Attribution 4.0 International (CC-BY-4.0). See the provided PDF on more information about the CC-BY-4.0.</p> <p>Version 1 contained an error in the global transformation matrix. Version 2 corrects this.</p>
Dataset for: Importance of satellite observations for high-resolution mapping of near-surface NO2 by machine learning
<p>Dataset for: Importance of satellite observations for high-resolution mapping of near-surface NO<sub>2 </sub>by machine learning</p> <p>This dataset is uploaded as a part of the article by Kim et al. (2021). The dataset is the hourly maps of near-surface nitrogen dioxide (NO<sub>2</sub>) concentrations at 100 m resolution for an Alpine domain (Switzerland and northern Italy, 6-12 °E, 42-48 °N). The dataset is provided per day (24 hours) in a netcdf (*.nc ~550MB). In this work, we have generated NO<sub>2 </sub>hourly maps for Feb. 2019 to May 2020 and, here, we upload for March 2019 only (~16 GB). If you need data for another period of time, please contact Gerrit Kuhlmann (gerrit.kuhlmann@empa.ch) or Minsu Kim (minsu.kim@empa.ch). </p>
Displacement measurements of the open-hardware sandbox using the AS5311 high-resolution magnetic sensor
<p>This dataset includes the experimental data from the AS5311 sensor for measuring the displacement of the Open-Hardware Geological Sandbox.</p> <p>These experiments are explained in the journal article: <a href="https://doi.org/10.1109/ACCESS.2023.3262617">Designing low-cost open-hardware electromechanical scientific equipment: A geological analogue modeling sandbox</a></p> <p>To understand this dataset, go to the Tectonic Open Hardware (TectOH) Sandbox project: <a href="https://github.com/URJCMakerGroup/TectOH">https://github.com/URJCMakerGroup/TectOH</a>. Then go to the <a href="https://github.com/URJCMakerGroup/TectOH/tree/main/optional">optional</a> folder and to the <a href="https://github.com/URJCMakerGroup/TectOH/tree/main/optional/as5311_magn_sens">magnetic sensor</a> folder.</p> <p>This data set contains two kind of files:</p> <ul> <li><strong>bin</strong>: raw binary files received from the AS5311 high resolution sensor. Although this sensor sends 12 bit data, we have truncated the most significant bits and receive only 8 bits (one byte). Therefore, each byte of these binary files is a measurement of the distance. Each distance increment corresponds to ~0.488nm (2mm/2048)</li> <li><strong>csv</strong>: csv files that can be opened with any spreadsheet app, such as Libreoffice Calc or Microsoft Excel, or even with a text editor. This file contains the processed data from the binary files. These files have been generated with the proc_magn_sensor.py Python script located in the <a href="https://github.com/URJCMakerGroup/TectOH">project repository</a>. There are some columns, which are: <ul> <li>index: measurement number</li> <li>time in milliseconds: each measurement is taken every 250 us</li> <li>median2: in micrometers, since the sensor may jitter, we have applied the median filter twice. All the data has been subtracted to the lowest value, making the lowest value equal to zero.</li> <li>median1: in micrometers, median filter only applied once. All the data has been subtracted to the lowest value, making the lowest value equal to zero.</li> <li>mean: in micrometers, mean filter. All the data has been subtracted to the lowest value, making the lowest value equal to zero.</li> <li>mean int: in micrometers, mean filter rounded to an integer value. All the data has been subtracted to the lowest value, making the lowest value equal to zero.</li> <li>orig_base: this is not in micrometers, but in the units of the sensor (~0.488nm). The only processing done is that when there is an overflow of 255 to 0, or from 0 to 255, it adds the overflow to continue the trend. All the data has been subtracted to the lowest value, making the lowest value equal to zero.</li> <li>original: this is the data received from the sensor with no processing, each value is ~0.488nm</li> <li>mean2: in micrometers, mean filter applied twice. All the data has been subtracted to the lowest value, making the lowest value equal to zero.</li> </ul> </li> </ul> <p>There are two set of experiments:</p> <ul> <li><strong>Experiments with no load</strong>. These files start with <em>noload_</em><br> In these experiments the gantry is moved 1 mm alternatively to the front and then reversing direction. Moving in this alternate way a few times. There are five experiments each of them with a different speed: v= 10 mm/h; 25 mm/h; 50 mm/h; 82 mm/h and 100 mm/h. The name of the file indicates the speed: <ol> <li>noload_100mmh_1mm: FBFBF: 1mm forth, 1mm back, 1mm forth, 1mm back, 1 mm forth</li> <li>noload_25mmh_1mm: FBFFBBFB</li> <li>noload_50mmh_1mm: FBFBFB</li> <li>noload_82mmh_1mm: FBFBFB</li> <li>noload_100mmh_1mm: FBFBFB</li> </ol> </li> <li><strong>Experiments pushing a 5kg sand load</strong>. These files start with <em>load5kg_</em> <ol> <li>load5kg_25mmh_5mm: moving 5kg at 25mm/h a distance of 5mm</li> <li>load5kg_25mmh_10mm: moving 5kg at 25mm/h a distance of 10mm</li> <li>load5kg_25mmh_20mm: moving 5kg at 25mm/h a distance of 20mm</li> <li>load5kg_75mmh_20mm: moving 5kg at 75mm/h a distance of 20mm</li> <li>load5kg_75mmh_50mm: moving 5kg at 75mm/h a distance of 50mm</li> <li>load5kg_100mmh_25mm: moving 5kg at 100mm/h a distance of 20mm</li> <li>load5kg_100mmh_50mm: moving 5kg at 100mm/h a distance of 50mm</li> </ol> </li> </ul> <p> </p> <p> </p> <p> </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.