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240 results for “High resolution maps”
Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"
<p>The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.</p> <p>All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.</p> <p>The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a></p> <p>The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a></p> <p>To obtain maximum compression of the data, the tar command used to generate this tarball was:</p> <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre> <p> </p>
Mapping past land cover on Poitiers in 1993 at Very High Resolution using GEOBIA approach and open data
<p>This dataset contains a land cover map of Poitiers in 1993 over an area of 225km².</p> <p>The land cover map was achieved using aerial images of the French National Geographic Institute (IGN) and Landsat-5 TM images combined with remote sensing methods. Geographic Object-Based Image Analysis (GEOBIA) and Random Forest classifications produced a reliable land cover map at a 1m of spatial resolution.</p> <p>Orthophotos produced as well as training and validating polygons to achieve the classifications were added into this dataset.</p> <p>As land cover changes is crucial to land management, this map will help to understand changes from 1993 to now for urban, agricultural issues but also their impact on ecological processes. Data will be easily used in GIS applications for any users.</p> <p>This work is part of the thesis of Elie Morin which was funded by la région Nouvelle-Aquitaine and Grand Poitiers Communauté urbaine, among others.</p>
High-Resolution Vegetation Height Maps for Switzerland in 2017-2020
<p>This dataset comprises 10m-resolution vegetation height maps for Switzerland spanning from 2017 to 2020. It encompasses both mean and maximum vegetation height data, generated through the integration of Sentinel-2 and airborne laser scanning information.</p>
Data from: High-resolution crossover maps for each bivalent of Zea mays using recombination nodules
<p>Recombination nodules (RNs) mark sites of crossing over along pachytene synaptonemal complexes (SCs). Thus, RNs provide the highest resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes because they are observed by electron microscopy. Using the maize inbred line KYS, we have prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4272 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. Average RN frequency per bivalent is closely correlated with SC length. The total length of the RN map is about two-fold shorter than most linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents.</p>
High-resolution mapping of the period landscape reveals polymorphism in cell cycle frequency tuning
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Data from: High-resolution crossover maps for each bivalent of Zea mays using recombination nodules
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Data and code for: A novel method for mapping high-precision animal locations using high-resolution imagery
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Molecular dynamics simulations in: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter
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Source Index Map Layer for High-Resolution Orthorectified Imagery from Approximately 1990, Niwot Ridge LTER Project Area, Colorado
Citation Manley, W.F., Parrish, E.G., and Lestak, L.R., 2009, High-Resolution Orthorectified Imagery and Digital Elevation Models for Study of Environmental Change at Niwot Ridge and Green Lakes Valley, Colorado: Niwot Ridge LTER, INSTAAR, University of Colorado at Boulder, digital media. This vector shapefile is a source index map layer for the mosaic of orthorectified aerial photography from 1988 and 1990 for the Niwot Ridge Long Term Ecological Research (LTER) project. The index also covers the Green Lakes Valley portion of the Boulder Creek Critical Zone Observatory (CZO). The index polygons are attributed with source photo date and photo year. The mosaic is derived from approx. 1:40,000 scale, color infrared (CIR) photographs acquired by the United States Geological Survery (USGS) National Aerial Photography Program (NAPP). Other datasets available in this series includes orthorectified aerial photograph mosaics (for 1953, 1972, 1985, approximately 1990, 1999, 2000, 2002, 2004, 2006 and 2008), digital elevation models (DEM's), and accessory map layers. Together, the DEM's and imagery will be of interest to students, research scientists, and others for observation and analysis of natural features and ecosystems. NOTE: This EML metadata file does not contain important geospatial data processing information. Before using any NWT LTER geospatial data read the arcgis metadata XML file in either ISO or FGDC compliant format, using ArcGIS software (ArcCatalog > description), or by viewing the .xml file provided with the geospatial dataset.
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>
Data for: High-resolution land value maps reveal underestimation of conservation costs in the United States
<p>The justification and targeting of conservation policy rests on reliable measures of public and private benefits from competing land uses. Advances in Earth system observation and modeling permit the mapping of public ecosystem services at unprecedented scales and resolutions, prompting new proposals for land protection policies and priorities. Data on private benefits from land use are not available at similar scales and resolutions, resulting in a data mismatch with unknown consequences. Here I show that private benefits from land can be quantified at large scales and high resolutions, and that doing so can have important implications for conservation policy models. I develop the first high-resolution estimates of fair market value of private lands in the contiguous United States by training tree-based ensemble models on 6 million land sales. The resulting estimates predict conservation cost with up to 8.5 times greater accuracy than earlier proxies. Studies using coarser cost proxies underestimated conservation costs, especially at the expensive tail of the distribution. This might have led to underestimations of policy budgets by factors of up to 37.5 in recent work. More accurate cost accounting will help policy makers acknowledge the full magnitude of contemporary conservation challenges, and can assist with the targeting of public ecosystem service investments.</p>
High spatial resolution mapping identifies habitat characteristics of the invasive vine Antigonon leptopus on St. Eustatius (Lesser Antilles)
<p>On the Caribbean island of St. Eustatius, Coralita (<i>Antigonon leptopus</i>)<i> </i>is an aggressive invasive vine posing major biodiversity conservation concerns. The generation of distribution maps can address these conservation concerns by helping to elucidate the drivers of invasion. We test the use of support vector machines to map the distribution of Coralita on St. Eustatius at high spatial resolution and use this map to identify potential landscape and geomorphological factors associated with Coralita presence. This latter step was performed by comparing the actual distribution of Coralita patches to a random distribution of patches. To train the support vector machine algorithm, we used three vegetation indices and seven texture metrics derived from a 2014 WorldView-2 image. The resulting map shows that Coralita covered 3.18% of the island in 2014, corresponding to an area of 64 ha. The mapped distribution was highly accurate, with 93.2% overall accuracy (Coralita class producer's accuracy: 76.4%, user's accuracy: 86.2%). Using this classification map, we found that Coralita is not randomly distributed across the landscape, occurring significantly closer to roads and drainage channels, in areas with higher accumulated moisture, and on flatter slopes. Coralita was found more often than expected in grasslands, disturbed forest and urban areas, but was relatively rare in natural forest. These results highlight the ability of high spatial resolution data from sensors such as WorldView-2 to produce accurate invasive species, providing valuable information for predicting current and future spread risks and for early detection and removal plans.</p>
Data from: High resolution spatial mapping of human footprint across Antarctica and its implications for the strategic conservation of avifauna
Human footprint models allow visualization of human spatial pressure across the globe. Up until now, Antarctica has been omitted from global footprint models, due possibly to the lack of a permanent human population and poor accessibility to necessary datasets. Yet Antarctic ecosystems face increasing cumulative impacts from the expanding tourism industry and national Antarctic operator activities, the management of which could be improved with footprint assessment tools. Moreover, Antarctic ecosystem dynamics could be modelled to incorporate human drivers. Here we present the first model of estimated human footprint across predominantly ice-free areas of Antarctica. To facilitate integration into global models, the Antarctic model was created using methodologies applied elsewhere with land use, density and accessibility features incorporated. Results showed that human pressure is clustered predominantly in the Antarctic Peninsula, southern Victoria Land and several areas of East Antarctica. To demonstrate the practical application of the footprint model, it was used to investigate the potential threat to Antarctica's avifauna by local human activities. Relative footprint values were recorded for all 204 of Antarctica's Important Bird Areas (IBAs) identified by BirdLife International and the Scientific Committee on Antarctic Research (SCAR). Results indicated that formal protection of avifauna under the Antarctic Treaty System has been unsystematic and is lacking for penguin and flying bird species in some of the IBAs most vulnerable to human activity and impact. More generally, it is hoped that use of this human footprint model may help Antarctic Treaty Consultative Meeting policy makers in their decision making concerning avifauna protection and other issues including cumulative impacts, environmental monitoring, non-native species and terrestrial area protection.
Comprehensive dataset from high resolution UAV land cover mapping of diverse natural environments in Serbia
<p>This dataset consists of raw RGB and NIR images captured using the DJI Inspire 1 UAV equipped with interchangeable RGB and NDVI-modified cameras. Data were collected across 27 diverse study sites in Serbia, representing a variety of ecological and landscape features. The UAV flights followed pre-defined grid missions, capturing high-resolution imagery with a ground sampling distance (GSD) of 3–4 cm. The collected images were processed to produce georeferenced orthomosaics, which serve as the basis for detailed land cover classification and analysis.</p>
NESEA-Rice10: high-resolution annual paddy rice maps for Northeast and Southeast Asia from 2017 to 2019
<p>This dataset provides annual paddy rice maps of Northeast and Southeast Asia from 2017 to 2019.</p> <p>*** The data file is in “.tif" format</p> <p>*** Spatial extent: Northeast and Southeast Asia</p> <p>*** Temporal Resolution: Yearly</p> <p>*** Pixel size: 10 m</p> <p>*** Projection information: EPSG: 4326</p> <p>*** CropType: Paddy rice.</p> <p>*** Year: Values from 2017 to 2019</p> <p>*** The file name consists of year (Y), latitude range (N/S), and longitude range (E). For example, the file name '2019Y_40_45N_140_145E' means the map of paddy rice in the range of 40-50 degrees North and 140-145 degrees East for 2019.</p>
High resolution dynamic mapping of the C. elegans intestinal brush border
<p>The intestinal brush border is made of an array of microvilli that increases the membrane surface area for nutrient processing, absorption, and host defense. Studies on mammalian cultured epithelial cells uncovered some of the molecular players and physical constrains required to establish this apical specialized membrane. However, the building and maintenance of a brush border <em>in vivo</em> has not been investigated in detail yet. Here, we combined super-resolution imaging, transmission electron microscopy and genome editing in the developing nematode <em>C. elegans</em> to build a high-resolution and dynamic localization map of known and new brush border markers. Notably, we show that microvilli components are dynamically enriched at the apical membrane during microvilli outgrowth and maturation but become highly stable once microvilli are built<em>.</em> This new toolbox will be instrumental to understand the molecular processes of microvilli growth and maintenance <em>in vivo</em> as well as the effect of genetic perturbations, notably in the context of disorders affecting brush border integrity.</p>
HAMSTER: Hyperspectral Albedo Maps dataset with high Spatial and TEmporal Resolution
<p>This dataset contains 365 hyperspectral albedo maps of Earth with a temporal resolution of 1 day. The hyperspectral albedo maps are built from a 10-year average of the MODIS Surface Reflectance dataset (MCD43D42-48, version 6.1). Using a Principal Component Analysis (PCA) regression algorithm we combine different hyperspectral laboratory and in-situ measurements datasets of various dry soils, vegetation surfaces and mixure of both to reconstruct the albedo maps in the entire wavelength range from 400 to 2500 nm. The hyperspectral albedo maps have a spatial resolution of 0.25° in latitude and longitude.</p> <p>Additional hyperspectral albedo maps with a coarser spatial and spectral resolutions are available in the "Data sets" supplemetary material of "HAMSTER: Hyperspectral Albedo Maps dataset with high Spatial and TEmporal Resolution" (Roccetti et al., 2024, https://doi.org/10.5194/egusphere-2024-167) or upon request to the corresponding author.</p>
Methodological approaches to identifying and mapping fields of specific crops on a basis of high-resolution satellite images
<p>Supplementary materials v2 for the article Unagaev A, Korotkova I and Efremova N. "Methodological approaches to identifying and mapping fields of specific crops on a basis of high-resolution satellite images using phenological, geographic and regional statistical information"<br> </p>
GDCLD:A globally distributed dataset of coseismic landslide mapping via multi-source high-resolution remote sensing images
<p>GDCLD : A globally distributed dataset of coseismic landslide mapping via multi-source high-resolution remote sensing images</p> <p>Fang, C., Fan, X., Wang, X., Nava, L., Zhong, H., Dong, X., Qi, J., and Catani, F.: A globally distributed dataset of coseismic landslide mapping via multi-source high-resolution remote sensing images, Earth Syst. Sci. Data Discuss. [preprint], https://doi.org/10.5194/essd-2024-239, in review, 2024.</p> <p> </p> <p>Data description:</p> <p> </p> <p>The training dataset and the validation dataset are composed of UAV, PlanetScope, Gaofen-6 and Map World images of the 5 earthquake regions of Luding, Nippes, Hokkaido, Jiuzhaigou and Mainling. There is no overlapping area in each TIFF. The training dataset and the validation dataset are randomly divided at a ratio of approximately 0.75:0.25.</p> <p> </p> <p>train_dataset:</p> <p>train_data: The train dataset part of the GDCLD data set contains 11162 data matrices (TIFF), and the shape of the matrix is (1024, 1024, 3) (TIFF).</p> <p>train_label: The train dataset part of the GDCLD data set contains 11162 data matrices (TIFF), and the shape of the matrix is (1024, 1024, 1) (TIFF).</p> <p> </p> <p>Validation_dataset</p> <p>val_data: The validation dataset part of the GDCLD data set contains 4459 data matrices (TIFF), and the shape of the matrix is (1024, 1024, 3) (TIFF).</p> <p>val_label: The validation dataset part of the GDCLD data set contains 4459 data matrices (TIFF), and the shape of the matrix is (1024, 1024, 1) (TIFF).</p> <p> </p> <p>Test_dataset (Lushan, Sumatra, Mesetas and Palu dataset)</p> <p>This package contains the original files of remote sensing images from three sources: UAV, Map World, and PlaneScope belonging to the Lushan, Sumatra, Mesetas and Palu earthquake regiones, which are used to display the test area.<br><br>Future work:<br>The future work includes additional landslide data that the authors will continue to upload. In this 2.0 version update, we have added UAV imagery and interpreted data for loess landslides triggered by the December 2023 M6.2 earthquake in Gansu, China, with a resolution of 0.1 m. Due to authorization constraints, we can only provide PNG files without geographic coordinates. Additionally, this update includes PlanetScope imagery of landslides induced by heavy rainfall in Guangdong, China, in 2024, as well as PlanetScope imagery and landslide labels for events triggered by the Hualien earthquake in Taiwan.<br><br>Please note that this landslide dataset is publicly available exclusively for scientific research purposes and must not be used for commercial purposes.</p>
Redefining floristic zones in the Korean Peninsula using high-resolution georeferenced specimen data and self-organizing maps
<p>The use of biota to analyze the distribution pattern of biogeographic regions is essential to gain a better understanding of the ecological processes that cause biotic differentiation and biodiversity at multiple spatiotemporal scales. Recently, the collection of high-resolution biological distribution data (e.g., specimens) and advances in analytical theory have led to the quantitative analysis and more refined spatial delineation of biogeographic regions. This study was conducted to redefine floristic zones in the southern part of the Korean Peninsula and to better understand the eco-evolutionary significance of the spatial distribution patterns. Based on 309,333 distribution data of 2,954 vascular plant species in the Korean Peninsula, we derived floristic zones using self-organizing maps. We compared the characteristics of the derived regions with those of historical floristic zones and ecologically important environmental factors (climate, geology, and geography). In the clustering analysis of the floristic assemblages, four distinct regions were identified, namely, the cold floristic zone (Zone I) in high-altitude regions at the center of the Korean Peninsula, cool floristic zone (Zone II) in high-altitude regions in the south of the Korean Peninsula, warm floristic zone (Zone III) in low-altitude regions in the central and southern parts of the Korean Peninsula, and maritime warm floristic zone (Zone IV) including the volcanic islands Jejudo and Ulleungdo. Totally, 1,099 taxa were common to the four floristic zones. Zone IV showed the highest abundance of specific plants (those found in only one zone), with 404 taxa. Our study improves floristic zone definitions using high-resolution regional biological distribution data. It will help better understand and re-establish regional species diversity. In addition, our study provides key data for hotspot analysis required for the conservation of plant diversity.</p>
ScienceDex guides
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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.