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53 results for “spatial methods”
Quantification of 3D spatial correlations between state variables and distances to the grain boundary network in full-field crystal plasticity spectral method simulations
<p>This repository provides supplementary material to our paper: <a href="https://doi.org/10.1088/1361-651X/ab7f8c">https://doi.org/10.1088/1361-651X/ab7f8c</a></p> <p><strong>DAMASKPhenoPowerLaw75x75x75TestCase.zip</strong><br> An exemplary DAMASK simulation and corresponding output, generated from DAMASK v2.0.3. We used this to debug more productively the implementation of the post-processing tools. Furthermore we employed this simulation in the paper to identify why the graph clustering grain reconstruction method in many cases fuses neighboring grains in similar orientation.</p> <p><strong>DAMASKPhenoPowerLaw256x256x256ProductionRun.zip</strong><br> All input to run the DAMASK simulation that we discussed in the paper.</p> <p><strong>DAMASKPDTSettings256x256x256ProductionRun.zip</strong><br> All damaskpdt settings files to execute the individual post-processing studies of the paper.</p> <p><strong>DAMASKPDTSlurmSubmissionScripts256x256x256ProductionRun.zip</strong><br> All SLURM scripts we used to execute the compilation of damaskpdt and post-processing on TALOS.</p> <p><strong>DAMASKPDTSlurmLogs256x256x256ProductionRun.zip</strong><br> All logs from the SLURM job management system from the individual post-processing runs.</p> <p><strong>DAMASKPDTSourceCode_USedForAnalyticalDistanceToVoronoiCellFacets.zip</strong><br> The source code to the tool we developed during the revision process of our paper to verify the methods<br> via computing analytically exact distances to the facets of the Poisson-Voronoi tessellation from the<br> DAMASK microstructure instantiation.<br> <br> <strong>DAMASKPDTSourceCode_Production.zip</strong><br> The source code we used to post-process all results from the DAMASK simulations.</p> <p><strong>GitHub repository:</strong><br> https://github.com/mkuehbach/damaskpdt</p>
"Is Heidi really happier in the mountains? A mixed-methods investigation of spatial affect in fiction." - Data
<p>This repository provides access to the data used in Grisot, G & Herrmann, J. B. (2024) "Is Heidi really happier in the mountains? A mixed-methods investigation of spatial affect in fiction"</p> <p>It contains the following datasets:</p> <ul> <li><a href="https://zenodo.org/api/records/14235844/draft/files/all_entities.csv/content" target="_blank" rel="noopener noreferrer">all_entities.csv</a>: the spatial entities lists used in the paper (see Grisot, G & Herrmann, J. B., 2023)</li> <li><a href="https://zenodo.org/api/records/14235844/draft/files/corpus_books_aggr_sent_norm.csv/content" target="_blank" rel="noopener noreferrer">corpus_books_aggr_sent_norm.csv</a>: a corpus of N=184 Swiss literary narrative texts written in German between 1822 and 1940 by 69 Swiss authors, with sentiment values and spatial entities identified in each sentence.</li> <li><a href="https://zenodo.org/api/records/14235844/draft/files/heidi_clean_aggr_sent.csv/content" target="_blank" rel="noopener noreferrer">heidi_clean_aggr_sent.csv</a>: the 1880 digitised edition of the novel <em>Heidi</em>, as available from E-Rara, with sentiment values and spatial entities identified in each sentence.</li> <li><a href="https://zenodo.org/api/records/14235844/draft/files/sentiart.csv/content" target="_blank" rel="noopener noreferrer">sentiart.csv</a>: the sentiment lexcon SentiArt (Jacobs, 2019)</li> </ul>
NURBS Enhanced Virtual Element Methods for the Spatial Discretisation of the Multigroup Neutron Diffusion Equation on Curvilinear Polygonal Meshes
<p>This repository holds all of the raw data generated by my C++ code for a paper "NURBS Enhanced Virtual Element Methods for the Spatial Discretisation of the Multigroup Neutron Diffusion Equation on Curvilinear Polygonal Meshes".</p> <p>The C++ code solves the neutron diffusion equation using a novel spatial discretisation called the Virtual Element Method.</p> <p>Alongside the raw data (stored in VTK and HDF5 files) are post-processing python scripts which read the raw data, compute meaningful quantities of interest and generate plots/figures.</p>
A method for generating coherent spatially explicit maps of seasonal palaeoclimates from site-based reconstructions
<p>Reconstruction of climate anomalies in southern Europe for the Last Glacial Maximum (LGM, ca 21,000 years ago), made by combining pollen based reconstructions (from Bartlein et al. 2011) and averaged outputs of LGM simulations from the 3rd round of the Palaeoclimate Model Intercomparison Project (PMIP, Braconnot et al. 2011), under a variational data assimilation technique. Reconstructions made using this technique are designed to be used for data-model comparison, specifically against the results of PMIP4. The dataset consists of 6 variables: moisture index (the ratio precipitation and equilibrium evapotranspiration), mean annual precipitation (mm), mean annual temperature (degrees C), mean temperature of the coldest month (degrees C), mean temperature of the warmest month (degrees C), growing degree days above 5 degrees C (day degrees C). The standard deviation of these variables is also given.</p>
reference genome used for scRNA-seq mapping with CellRanger in the method spatial-scERA
<p>The modified <em>Drosophila </em>melanogaster (dm6) reference genome used for the mapping with CellRanger in the method paper about spatial-scERA</p> <p>The genome is composed of the original genome from EnsembleMetazo website (BDGP6.46.110). An addition of 26 chromosomes (one for the plasmid construct and 25 for the tested enhancer sequences) is also present to allow for the mapping of mRNAs comming from our constructs. </p>
Рис. 8. 3D–диаграммы пространственного распределениЯ обилиЯ моллюска M. catrusiana (А), фитомассы (В), твердости грунта на глубине 5–10 см (C) и доли агрегатных фракций 3–5 мм (D) на участке № 2 в 2011 г. (единицы иЗмерениЯ осей Х и Y даны в метрах). Fig. 8. 3D–diagrams of the abundance spatial distribution of the land snail M. catrusiana (A), phytomass (B), 0–10 cm layer soil penetration resistance (C), aggregate particle size 3–5 mm (D) at the site 1 in 2011 (axes X and Y presented in meters). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 8. 3D–диаграммы пространственного распределениЯ обилиЯ моллюска M. catrusiana (А), фитомассы (В), твердости грунта на глубине 5–10 см (C) и доли агрегатных фракций 3–5 мм (D) на участке № 2 в 2011 г. (единицы иЗмерениЯ осей Х и Y даны в метрах). Fig. 8. 3D–diagrams of the abundance spatial distribution of the land snail M. catrusiana (A), phytomass (B), 0–10 cm layer soil penetration resistance (C), aggregate particle size 3–5 mm (D) at the site 1 in 2011 (axes X and Y presented in meters).
Рис. 6. Графики Зависимости оценок варианс (S2) от средней плотности (D) популЯций наЗемных моллюсков B. cylindrica (А) и M. cartusiana (В): 1 – участок № 1, 2010 г.; 2 – участок № 2, 2011 г.; 3 – участок № 4, 2012 г.; 4 – участок № 5, 2012 г. Fig. 6. Variance estimation (S2) and average density (D) of the land snail B. cylindrica (А) and M. cartusiana (В) population scatter plots: 1 – site 1, 2010; 2 – site 2, 2011; 3 – site 4, 2012; 4 – site 5, 2012. in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 6. Графики Зависимости оценок варианс (S2) от средней плотности (D) популЯций наЗемных моллюсков B. cylindrica (А) и M. cartusiana (В): 1 – участок № 1, 2010 г.; 2 – участок № 2, 2011 г.; 3 – участок № 4, 2012 г.; 4 – участок № 5, 2012 г. Fig. 6. Variance estimation (S2) and average density (D) of the land snail B. cylindrica (А) and M. cartusiana (В) population scatter plots: 1 – site 1, 2010; 2 – site 2, 2011; 3 – site 4, 2012; 4 – site 5, 2012.
Рис. 5. Коррелограммы покаЗателей обилиЯ наЗемных моллюсков раЗных воЗрастных групп (1 – ювенильные; 2 – вЗрослые; 3 – все вместе): A – H. lucorum, участок № 1, 2010 г.; B – Ch. tridens, участок № 2, 2011 г.; C – Ch. tridens, участок № 4, 2012 г.); D – Ch. tridens, участок № 5, 2012 г. (достоверные оценки индекса Морана отмечены Залитыми Значками). Fig. 5. Spatial correlogram of the land snail different age groups abundance (1 – juvenile; 2 – adult; 3 – total): A – H. lucorum, site 1, 2010; B – Ch. tridens, site 2, 2011; C – Ch. tridens, site 4, 2012; D – Ch. tridens, site 5, 2012 (Moran index confidence value presented by filled signs). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 5. Коррелограммы покаЗателей обилиЯ наЗемных моллюсков раЗных воЗрастных групп (1 – ювенильные; 2 – вЗрослые; 3 – все вместе): A – H. lucorum, участок № 1, 2010 г.; B – Ch. tridens, участок № 2, 2011 г.; C – Ch. tridens, участок № 4, 2012 г.); D – Ch. tridens, участок № 5, 2012 г. (достоверные оценки индекса Морана отмечены Залитыми Значками). Fig. 5. Spatial correlogram of the land snail different age groups abundance (1 – juvenile; 2 – adult; 3 – total): A – H. lucorum, site 1, 2010; B – Ch. tridens, site 2, 2011; C – Ch. tridens, site 4, 2012; D – Ch. tridens, site 5, 2012 (Moran index confidence value presented by filled signs).
Рис. 4. Коррелограммы покаЗателей обилиЯ наЗемного моллюска M. cartusiana раЗных воЗрастных групп (1 – ювенильные; 2 – вЗрослые; 3 – все вместе): A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.); D – участок № 5, 2012 г. (достоверные оценки индекса Морана отмечены Залитыми Значками). Fig. 4. Spatial correlogram of land snail M. cartusiana age groups abundance (1 – juvenile; 2 – adult; 3 – total): A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Moran index confidence value presented by filled sings). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 4. Коррелограммы покаЗателей обилиЯ наЗемного моллюска M. cartusiana раЗных воЗрастных групп (1 – ювенильные; 2 – вЗрослые; 3 – все вместе): A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.); D – участок № 5, 2012 г. (достоверные оценки индекса Морана отмечены Залитыми Значками). Fig. 4. Spatial correlogram of land snail M. cartusiana age groups abundance (1 – juvenile; 2 – adult; 3 – total): A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Moran index confidence value presented by filled sings).
Рис. 3. Коррелограммы покаЗателей обилиЯ наЗемного моллюска B. cylindrica раЗных воЗрастных групп (1 – ювенильные; 2 – вЗрослые; 3 – все вместе): A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.); D – участок №5, 2012 г. (достоверные оценки индекса Морана отмечены Залитыми Значками). Fig. 3. Spatial correlogram of the land snail B. cylindrica age groups abundance (1 – juvenile; 2 – adult; 3 – total): A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Moran index confidence value presented by filled signs). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 3. Коррелограммы покаЗателей обилиЯ наЗемного моллюска B. cylindrica раЗных воЗрастных групп (1 – ювенильные; 2 – вЗрослые; 3 – все вместе): A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.); D – участок №5, 2012 г. (достоверные оценки индекса Морана отмечены Залитыми Значками). Fig. 3. Spatial correlogram of the land snail B. cylindrica age groups abundance (1 – juvenile; 2 – adult; 3 – total): A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Moran index confidence value presented by filled signs).
Рис. 7. 3D–диаграммы пространственного распределениЯ обилиЯ моллюска B. cylindrica (А), фитомассы (В), проективного покрытиЯ (С), твердости грунта на глубине 5–10 см (D) на участке № 1 в 2010 г. (единицы иЗмерениЯ осей Х и Y даны в метрах). Fig. 7. 3D–diagrams of the abundance spatial distribution of the snail B. cylindrica (A), phytomass (B), plants projective cover (C), 0–10 cm layer soil penetration resistance (D) at the site 1 in 2010. (axes X and Y presented in meters). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 7. 3D–диаграммы пространственного распределениЯ обилиЯ моллюска B. cylindrica (А), фитомассы (В), проективного покрытиЯ (С), твердости грунта на глубине 5–10 см (D) на участке № 1 в 2010 г. (единицы иЗмерениЯ осей Х и Y даны в метрах). Fig. 7. 3D–diagrams of the abundance spatial distribution of the snail B. cylindrica (A), phytomass (B), plants projective cover (C), 0–10 cm layer soil penetration resistance (D) at the site 1 in 2010. (axes X and Y presented in meters).
Рис. 2. Диаграммы распределениЯ обилиЯ наЗемного моллюска M. cartusiana: A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.; D – участок № 5, 2012 г. (единицы иЗмерениЯ осей Х и Y даны в метрах; численность особей пропорциональна раЗмерам Шариков). Fig. 2. Diagram of the abundance distribution of the land snail M. cartusiana: A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Х and Y axes presented in meters; abundance proportional to sphere sizes). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 2. Диаграммы распределениЯ обилиЯ наЗемного моллюска M. cartusiana: A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.; D – участок № 5, 2012 г. (единицы иЗмерениЯ осей Х и Y даны в метрах; численность особей пропорциональна раЗмерам Шариков). Fig. 2. Diagram of the abundance distribution of the land snail M. cartusiana: A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Х and Y axes presented in meters; abundance proportional to sphere sizes).
Fig. 1 in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Fig. 1. Diagram of the abundance distribution of the land snail B. cylindrica: A – site 1, 2010; B – site 2, 2011; C – site 4, 2012; D – site 5, 2012 (Х and Y axes presented in meters; abundance proportional to sphere sizes).
Рис. 1. Диаграммы распределениЯ обилиЯ наЗемного моллюска B. cylindrica: A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.; D – участок № 5, 2012 г. (единицы иЗмерениЯ осей Х и Y даны в метрах; численность особей пропорциональна раЗмерам Шариков). in Analysis of the spatial distribution patterns of the land snail populations: a geostatistic method approach
Рис. 1. Диаграммы распределениЯ обилиЯ наЗемного моллюска B. cylindrica: A – участок № 1, 2010 г.; B – участок № 2, 2011 г.; C – участок № 4, 2012 г.; D – участок № 5, 2012 г. (единицы иЗмерениЯ осей Х и Y даны в метрах; численность особей пропорциональна раЗмерам Шариков).
Boosting multiplexing capabilities for error-robust spatial transcriptomic methods using a set exchange approach
Open the record for dataset details and reuse information.
SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections (Revision data)
<p>The submitted dataset, correspond to the RAW (*.czi format) and analysis files of the <strong>revisions</strong> of 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>
Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
<p>A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of <i>Stipa</i><i> grandis</i> in grazed and ungrazed <i>S. grandis</i> communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of <i>S. grandis</i> by using the pair correlation function <i>g</i>(<i>r</i>) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of <i>S. grandis</i> were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.</p>
Mesosphere/lower thermosphere 3-dimensional spatially resolved winds observed by Chinese multistatic meteor radar network using the newly developed VVP method
<p>This dataset supports the article "Mesosphere/lower thermosphere 3-dimensional spatially resolved winds observed by Chinese multistatic meteor radar network using the newly developed VVP method" . The data are provided in MatLab format.</p>
Spatial-DC: a robust deep learning-based method for deconvolution of spatial proteomics
<p>The processed reference and spatial proteomics datasets, along with the processed mIHC imaging data of mouse PDAC tissue are available in the repository.</p> <p>Also, the source code for pre-processing, data analysis, and generating figure and tables has been deposited in both GitHub [<a href="https://github.com/TencentAILabHealthcare/Spatial-DC">https://github.com/TencentAILabHealthcare/Spatial-DC</a>] and Zenodo [<a href="https://doi.org/10.5281/zenodo.14386585">https://doi.org/10.5281/zenodo.14386585</a>].</p> <p> </p>
Light and malaise traps tell different stories about the spatial variations in arthropod biomass and method-specific insect abundance
<p><span>1. Conclusions reached in meta-analyses of changes in insect communities may be influenced by method-specific sampling biases, which may lead to inappropriate conservation measures.</span></p> <p><span>2. </span><span>We argue that the contradictory conclusions regarding terrestrial insect biomass, abundance and richness patterns are, at least partly, due to methodological limitations that reflect taxon-specific responses to environmental changes.</span></p> <p><span>3. </span><span>In this study, light and Malaise traps were simultaneously deployed to sample insects at 52 plots in a temperate forest in Germany along gradients of elevation (> 1000 m) and canopy openness (3 - 100 %). These gradients were used as predictors in models of total arthropod biomass according to the two trapping methods, and in models of abundance and richness of three commonly targeted groups: nocturnal moths, sampled using light traps, and hoverflies and bees, collected with Malaise traps.</span></p> <p><span>4. </span><span>A comparison of the total arthropod biomass obtained with the two methods revealed contrary results along the canopy openness gradient. Biomass in light traps showed a decreasing trend with increasing canopy openness while biomass in Malaise traps increased. The same opposing pattern was found for the abundance of selected taxa.</span></p> <p><span>5. </span><span>The different patterns describing spatial variation of arthropod communities obtained using light and Malaise traps can be explained by differences in the taxa predominantly collected. Regarding the ongoing debate on insect decline, our results demonstrate that comparing different taxa from different taxon-specific traps is inappropriate. Thus, we recommend that future meta-analyses take into account the sampling methods and taxon-specific responses to environmental changes.</span></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.