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196 results for “Spatial map”
Spatial mapping of root systems reveals diverse strategies of soil exploration and resource contest in grassland plants
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Data from: Abiotic proxies for predictive mapping of near-shore benthic assemblages: implications for marine spatial planning
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Data from: Retinotopic-like maps of spatial sound in primary 'visual' cortex of blind human echolocators
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Data from: Mapping spatial patterns to energetic benefits in groups of flow-coupled swimmers
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Data from: Mapping the spatial heterogeneity of watershed ecosystems and water quality in rainforest fjordlands
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Spatial probability maps of the superior parietal sulcus in the human brain
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SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections
<p>The submitted dataset, correspond to the RAW (*.czi format) and analysis files of the manuscript "SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections", which has been processed for revision (2020-01-31) by PLOS Biology.</p> <p>The files are in *.zip format and the naming follows thenumbering of the manuscript figures, which will be found in bioRxiv.org (<strong>ID#: BIORXIV/2020/938571</strong>). Each *.zip files contains a document with the description of all the provided files.</p>
Mapping the Local Spatial Charge in Defective Diamond by Means of N-V Sensors—A Self-Diagnostic Concept
<p>Mapping the Local Spatial Charge in Defective Diamond by Means of N-V Sensors—A Self-Diagnostic Concept</p> <p>Electrically active defects have a significant impact on the performance of electronic devices based on wide-band-gap materials. This issue is ubiquitous in diamond science and technology, since the presence of charge traps in the active regions of different classes of diamond-based devices (detectors, power diodes, transistors) can significantly affect their performance, due to the formation of space charge, memory effects, and the degradation of the electronic response associated with radiation-induced damage. Among the most common defects in diamond, the nitrogen-vacancy (N-V) center possesses unique spin properties that enable high-sensitivity field sensing at the nanoscale. Here, we demonstrate that N-V ensembles can be successfully exploited to perform direct local mapping of the internal electric-field distribution of a graphite-diamond-graphite junction exhibiting electrical properties dominated by trap- and space-charge-related conduction mechanisms. By means of optically detected magnetic resonance measurements, we performed both point-by-point readout and spatial mapping of the electric field in the active region at different bias voltages. In this novel “self-diagnostic” approach, defect complexes represent not only the source of detrimental space-charge effects but also a unique tool for their direct investigation, by providing an insight on the conduction mechanisms that could not be inferred in previous studies on the basis of conventional electrical and optical characterization techniques.</p>
The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets
<p>High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (<em>Entosphenus tridentatus</em>) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations likely explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent datasets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.</p>
Data for "TrueEBSD: correcting spatial distortions in electron backscatter diffraction maps"
<p>Data for "TrueEBSD: correcting spatial distortions in electron backscatter diffraction maps" published in Ultramicroscopy.</p> <p>Journal DOI: <a href="https://doi.org/10.1016/j.ultramic.2020.113130">https://doi.org/10.1016/j.ultramic.2020.113130</a>;<br> Preprint DOI: <a href="https://arxiv.org/abs/1909.00347">https://arxiv.org/abs/1909.00347</a>.</p> <p>The zipped folder contains:</p> <ol> <li>Readme (text file)</li> <li>'Ti-64' data subfolder: data for one of the maps in the Ti-64 map stitching example</li> <li>'ZrH' data subfolder: data for the hydride-containing Zircaloy-4 example</li> <li>'CP-Zr' data subfolder: data for the in-situ deformed Zr example</li> <li> 'MATLAB scripts' subfolder: TrueEBSD source code.</li> </ol> <p> </p> <p>Each data subfolder contains:</p> <ul> <li>Input image files</li> <li>EBSD orientation files in Bruker CTF format</li> <li>'Outputs' subfolder containing output figures as image files.</li> </ul> <p>The 'MATLAB scripts' subfolder contains TrueEBSD source code:</p> <ul> <li>The primary user interface is 'input_deck.m'. Most user settings can be changed here. <ul> <li>The input deck entries here have been pre-filled for the Ti-64 dataset.</li> </ul> </li> <li>To use TrueEBSD, run 'input_deck.m' in MATLAB.</li> <li>The method is outlined in 'main.m', which calls functions in 'MATLAB scripts\code\'.</li> </ul>
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.
Data from: Spatial structure of above-ground biomass limits accuracy of carbon mapping in rainforest but large scale forest inventories can help to overcome
Precise mapping of above-ground biomass (AGB) is a major challenge for the success of REDD+ processes in tropical rainforest. The usual mapping methods are based on two hypotheses: a large and long-ranged spatial autocorrelation and a strong environment influence at the regional scale. However, there are no studies of the spatial structure of AGB at the landscapes scale to support these assumptions. We studied spatial variation in AGB at various scales using two large forest inventories conducted in French Guiana. The dataset comprised 2507 plots (0.4 to 0.5 ha) of undisturbed rainforest distributed over the whole region. After checking the uncertainties of estimates obtained from these data, we used half of the dataset to develop explicit predictive models including spatial and environmental effects and tested the accuracy of the resulting maps according to their resolution using the rest of the data. Forest inventories provided accurate AGB estimates at the plot scale, for a mean of 325 Mg.ha-1. They revealed high local variability combined with a weak autocorrelation up to distances of no more than10 km. Environmental variables accounted for a minor part of spatial variation. Accuracy of the best model including spatial effects was 90 Mg.ha-1 at plot scale but coarse graining up to 2-km resolution allowed mapping AGB with accuracy lower than 50 Mg.ha-1. Whatever the resolution, no agreement was found with available pan-tropical reference maps at all resolutions. We concluded that the combined weak autocorrelation and weak environmental effect limit AGB maps accuracy in rainforest, and that a trade-off has to be found between spatial resolution and effective accuracy until adequate "wall-to-wall" remote sensing signals provide reliable AGB predictions. Waiting for this, using large forest inventories with low sampling rate (<0.5%) may be an efficient way to increase the global coverage of AGB maps with acceptable accuracy at kilometric resolution.
Data from: Range-wide spatial mapping reveals convergent character displacement of bird song
A long-held view in evolutionary biology is that character displacement generates divergent phenotypes in closely related coexisting species to avoid the costs of hybridisation or ecological competition, whereas an alternative possibility is that signals of dominance or aggression may instead converge to facilitate coexistence among ecological competitors. Although this counter-intuitive process⎯termed convergent agonistic character displacement⎯is supported by recent theoretical and empirical studies, the extent to which it drives spatial patterns of trait evolution at continental scales remains unclear. By modeling variation in song structure of two ecologically similar species of Hypocnemis antbird across Western Amazonia, we show that their territorial signals converge such that trait similarity peaks in the sympatric zone, where intense interspecific territoriality between these taxa has previously been demonstrated. We also use remote sensing data to show that signal convergence is not explained by environmental gradients and is thus unlikely to evolve by sensory drive (i.e. acoustic adaptation to the sound transmission properties of habitats). Our results suggest that agonistic character displacement driven by interspecific competition can generate spatial patterns opposite to those predicted by classic character displacement theory, and highlight the potential role of social selection in shaping geographical variation in signal phenotypes of ecological competitors.
Data from: Uncovering spatial variation in acoustic environments using sound mapping
Animals select and use habitats based on environmental features relevant to their ecology and behavior. For animals that use acoustic communication, the sound environment itself may be a critical feature, yet acoustic characteristics are not commonly measured when describing habitats and as a result, how habitats vary acoustically over space and time is poorly known. Such considerations are timely, given worldwide increases in anthropogenic noise combined with rapidly accumulating evidence that noise hampers the ability of animals to detect and interpret natural sounds. Here, we used microphone arrays to record the sound environment in three terrestrial habitats (forest, prairie, and urban) under ambient conditions and during experimental noise introductions. We mapped sound pressure levels (SPLs) over spatial scales relevant to diverse taxa to explore spatial variation in acoustic habitats and to evaluate the number of microphones needed within arrays to capture this variation under both ambient and noisy conditions. Even at small spatial scales and over relatively short time spans, SPLs varied considerably, especially in forest and urban habitats, suggesting that quantifying and mapping acoustic features could improve habitat descriptions. Subset maps based on input from 4, 8, 12 and 16 microphones differed slightly (< 2 dBA/pixel) from those based on full arrays of 24 microphones under ambient conditions across habitats. Map differences were more pronounced with noise introductions, particularly in forests; maps made from only 4-microphones differed more (> 4 dBA/pixel) from full maps than the remaining subset maps, but maps with input from eight microphones resulted in smaller differences. Thus, acoustic environments varied over small spatial scales and variation could be mapped with input from 4–8 microphones. Mapping sound in different environments will improve understanding of acoustic environments and allow us to explore the influence of spatial variation in sound on animal ecology and behavior.
Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing - Image and In SItu Sequencing data
<p>Image and ISS data for Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.</p><p>Image data consists of:</p><ul><li>Nucler stain (DAPI)</li><li>Masks for liver, rim and tumor regions</li><li>H&E images of parallel tissue sections</li></ul><p>Gene and cluster marker data is collected in the <i>markers.h5ad</i> file which can be read using AnnData (<a href="https://anndata.readthedocs.io/en/latest/">https://anndata.readthedocs.io/en/latest/)</a>. </p><p> </p>
Spatial Mapping for Visually Impaired Individuals
<p>By understanding the strengths and limitations of different assistive devices, blind individuals can make informed choices to improve their independence and quality of life.</p>
Processed Data 1 : Spatial multi-omic map of human myocardial infarction
<p>We provide here the processed snRNA-seq, snATAC-seq, and visium data for the manuscript: Kuppe, Ramirez Flores, Li et al. "Spatial multi-omic map of human myocardial infarction", 2022</p>
Supplementary material 1 from: Nedkov S, Zhiyanski M, Dimitrov S, Borisova B, Popov A, Ihtimanski I, Yaneva R, Nikolov P, Bratanova-Doncheva S (2017) Mapping and assessment of urban ecosystem condition and services using integrated index of spatial structure. One Ecosystem 2: e14499. https://doi.org/10.3897/oneeco.2.e14499
Figure representing examples of catalogues used during the identification built and land cover types.
Supplementary material 2 from: Nedkov S, Zhiyanski M, Dimitrov S, Borisova B, Popov A, Ihtimanski I, Yaneva R, Nikolov P, Bratanova-Doncheva S (2017) Mapping and assessment of urban ecosystem condition and services using integrated index of spatial structure. One Ecosystem 2: e14499. https://doi.org/10.3897/oneeco.2.e14499
Table representing all combinations of the integrated index of spatial structute in urban ecosystems in Bulgaria
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.