Find research datasets worth reusing

HR-GLDD: A globally distributed high resolution landslide dataset

HR-GLDD, a high-resolution (HR) dataset for landslide mapping composed of landslide instances from ten different physiographical regions globally: South and South-East Asia, East Asia, South America, and Central America. The dataset contains five rainfall triggered and five earthquake-triggered multiple landslide events that occurred in varying geomorphological and topographical regions.

opencc-by-4.0Jul 2022View details →

Project files provided as supporting information to the manuscript "Fast, accurate, and system-specific variable-resolution modelling of proteins"

Project files provided as supporting information to the manuscript "Fast, accurate, and system-specific variable-resolution modelling of proteins". The dataset contains the following files: - RMSD_adk: files containing the root-mean-square deviation computed on the C-alpha atoms/beads in the atomistic and CANVAS simulations of adk (Figure 6). - RMSF_adk: files containing the root-mean-square fluctuations of the C-alpha atoms/beads in the atomistic and CANVAS simulations of adk (Figure 6). - APBS_adk: PQR file of the system and DX file of the surface potential, for both the atomistic and CANVAS systems (Figure 7). - SASA_antibody: files containing the per-residue solvent accessible surface area of the atomistic region of the ake protein, in the atomistic and CANVAS simulations (Figure 8). - RMSF_antibody: files containing the root-mean-square fluctuations of the C-alpha atoms/beads in the atomistic and CANVAS simulations of antibody (Figure 9). - APBS_antibody: PQR file of the system and DX file of the surface potential, for both the atomistic and CANVAS systems (Figure 10). - SASA_antibody: files containing the per-residue solvent accessible surface area of the hinge region of the antibody for each conformational cluster, in the atomistic and CANVAS simulations (Figure 11). - RMSIP_antibody: RMSIP between the essential subspaces computed from the atomistic and CANVAS simulations (Figure S3). - rgyr_antibody: files containing the radii of gyration of the antibody for each conformational cluster, in the atomistic and CANVAS simulations (Figure S4). - ake_AA.mp4: video of the all-atom simulation of adenylate kinase - ake_canvas.mp4: video of the canvas simulation of adenylate kinase

Datasets for "High-resolution, basin-scale simulations reveal the impact of intermediate zonal jets on the Atlantic oxygen minimum zones".

This repository contains the 7-year averaged files from runs TATL10 and TATL3 used in the manuscript "High-resolution, basin-scale simulations reveal the impact of intermediate zonal jets on the Atlantic oxygen minimum zones". Additional files include the CARS oxygen climatology and the CMEMS model output used in the study.

Dataset for High-resolution mantle flow models reveal importance of plate boundary geometry and slab pull forces on generating tectonic plate motions

This repository contains the plugin and dataset used to setup models in the manuscript: "High-resolution mantle flow models reveal importance of plate boundary geometry and slab pull forces on generating tectonic plate motions". The material model plugin used in our models is in the "plugins" folder. The "models" folder contains the reference input parameter file described in the paper. All other model configurations shown in the paper can be obtained by modifying this parameter file.  The input files used to set up the models are in the respective folder. Additionally, the Jupyter notebook used to compute residuals of our models is provided in the "scripts" folder.

Dataset 2 for the reproduction of figures used in "High-resolution, basin-scale simulations reveal the impact of intermediate zonal jets on the Atlantic oxygen minimum zones""

This is the second dataset with data necessary for the reproduction of the figures used in the manuscript.

Daily satellite and gauge observed rainfall dataset (1980-2019) for Oman at 1km spatial resolution in GeoTIFFs

This is a re-gridded daily TRMM datasets. It has been resampled to 1km spatial resolution. The datasets have also been projected to UTM 40N

opencc-by-4.0Oct 2017View details →

High-resolution cone-beam scan of a pomegranate with two dosage levels

We release two tomographic scans of a pomegranate with two levels of radiation dosage for noise-level comparative studies in data analysis, reconstruction or segmentation methods. The dataset collected with higher dosage is referred to as the "good" dataset; and the other as the "noisy" dataset, as a way to distinguish between the two dosage levels.    The dataset are acquired using the custom built and highly flexible CT scanner, FlexRay Lab, developed by XRE NV and located at CWI. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1943-by-1535 pixels, 14-bit, flat detector panel.    Both dataset were collected over a 360 degrees in circular and continuous motion with 501 projections distributed evenly over the full circle. The uploaded dataset are not binned or normalized; a single dark and two (pre- and post-) flat fields are included for each scan. Projections for both sets were collected with 100 ms exposure time with the good data projections averaged over 5 takes, and no averaging was made for the noisy data. The tube settings for the good and noisy dataset were 70kV, 45W and 50kV, 20W, respectively. The total scanning time were 7 minutes for the good; 3 minutes for the noisy scan. Each dataset is packaged with the full list of data and scan settings files (in .txt format). These files contain the tube settings, scan geometry and full list of motor settings.   These dataset are produced by the Computational Imaging members at Centrum Wiskunde & Informatica (CI-CWI). For any useful Python/MATLAB scripts for FlexRay dataset, we refer the reader to our group's <a href="http://github.com/cicwi">GitHub page</a>.   For more information or guidance in using these dataset, please get in touch with  <ul> <li>s.b.coban [at] cwi.nl</li> </ul>

opencc-by-4.0Nov 2023View details →

ICTP-MOM5 driven by JRA55-do surface dataset at 1-degree and 0.25-degree horizontal resolution

Output files from MOM5 simulations driven by JRA55-do surface dataset following the OMIP-2 protocol.   Datasets include monthly data from the sixth cycle for: 1/ MOM5-LR: MOM5 at 1-degree resolution driven by JRA55-do. 2/ MOM5-HR: MOM5 at 0.25-degree resolution driven by JRA55-do 3/ MOM5-LR-winds: as in 1/ but using CORE-II zonal and meridional surface winds 4/ MOM5-LR-heat: as in 1/ but using CORE-II shortwave and longwave fluxes 5/ MOM5-anom: as in 1/ but using JRA55-do climatological surface winds plus monthly anomalies from CORE-II

opencc-by-4.0Apr 2024View details →

An Automated Method for Measuring Tree Rings Based on Super Resolution and Image Segmentation

Open the record for dataset details and reuse information.

opencc-by-4.0Jan 2024View details →

Radiographic data of a wooden block with metal markers at the FleX-ray laboratory (high resolution)

Summary This submission contains radiographic data containing metal markers of a small wooden block.   The data is made available as part of [Bossema et al., 2024].   Apparatus The dataset is acquired using the custom-built and highly flexible CT scanner, FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. This apparatus consists of a cone-beam microfocus X-ray point source that projects polychromatic X-rays onto a 1944-by-1536 pixels, 14-bit, flat detector panel. Full details can be found in [Coban 2020]. List of Contents The content of the submission is given below. All raw data (i.e. no corrections) is made available in .tif format. The data folder contains: <ul> <li>darkfield  image, di000000.tif,</li> <li>flatfield  image before acquisition, io000000.tif, and after acquisition, io000001.tif,</li> <li>raw (unprocessed or uncorrected) projections, scan_*.tif,</li> <li>data settings XRE.txt, a text file with scanner metadata,</li> <li>scan settings.txt, a text file with scanner metadata in more human readable format, and</li> <li>data settings XRE.ini, a snapshot text file of basic geometry information at the start of a scan.</li> <li>script_executed.txt, the text file containing the list of commands the apparatus has executed.</li> </ul>   Additional Links These datasets are produced by the <a>Computational Imaging group</a> at Centrum Wiskunde & Informatica (CI-CWI). For any relevant Python/MATLAB scripts for the FleX-ray datasets, we refer the reader to our group's <a>GitHub page</a>.   Contact Details For more information or guidance in using these datasets, please get in touch with  <ul> <li>bossema [at] cwi.nl</li> </ul>   Acknowledgments The authors would like to acknowledge the funding from the Netherlands Organisation for Scientific Research (NWO), project numbers 341-60-001, 639.073.506 and 628.007.033 and Netherlands Institute for Conservation, Art and Science (NICAS). References S. B. Coban, F. Lucka, W. J. Palenstijn, D. Van Loo, and K. J. Batenburg, “Explorative imaging and its implementation at the FleX-ray Laboratory,” J. Imaging, vol. 6, no. 18, 2020, doi: 10.3390/jimaging6040018. <a href="https://www.nature.com/articles/s41467-024-48102-w">Bossema, F.G., Palenstijn, W.J., Heginbotham, A. et al. Enabling 3D CT-scanning of cultural heritage objects using only in-house 2D X-ray equipment in museums. Nat Commun 15, 3939 (2024). https://doi.org/10.1038/s41467-024-48102-w</a>

Boron elemental and isotopic determination via the BF diatomic molecule using high-resolution continuum source graphite furnace molecular absorption spectrometry

This dataset contains the raw data corresponding to the figures of the publication DOI: 10.1039/d3ja00420a

opencc-by-4.0Apr 2024View details →

Spatial multiomic landscape of the human placenta at molecular resolution

Successful pregnancy and healthy human embryo development rely directly on the placenta’s complex, dynamic gene regulatory networks, both within placental subtypes and at the maternal-fetal interface (MFI), that underlie stemness, proliferation, differentiation, invasion, immune tolerance, and communication. These cellular and molecular mechanisms are notoriously challenging to elucidate and make this organ arguably the least understood in the human body. Additionally, disruption of this vast collection of intercellular and intracellular programs and pathways leads to pregnancy complications and developmental defects. Here, we generated a comprehensive spatially resolved multi-modal cell census elucidating the molecular architecture of the first trimester human placenta. We utilized paired single-cell ATAC and RNA sequencing, spatial single-cell ATAC and RNA sequencing (Slide-tags), and in situ sequencing and hybridization mapping of transcriptomes at molecular resolution (STARmap-ISS and STARmap-ISH) using 922,961 cells to construct a spatial single-cell atlas outlining joint epigenomic and transcriptomic regulatory dynamics. Paired analyses unraveled intricate tumor-like gene expression and transcription factor motif programs sustaining the placenta in a hostile uterine environment; further investigation of gene-linked cis-regulatory elements revealed heightened regulatory complexity governing trophoblast differentiation and placental disease risk. Complementary spatial mapping techniques decoded these programs within the placental villous core and extravillous trophoblast (EVT) cell column architecture while simultaneously revealing niche-establishing transcriptional elements and cell-cell communication. To unify our datasets, we computationally imputed 33,357-gene multiomic single-cell profiles and spatially characterized the placental chromatin accessibility landscape. This spatially resolved single-cell multiomic framework of the first trimester human placenta at molecular resolution serves as a blueprint for future studies investigating cellular and molecular programs regulating early placental development and pregnancy.

dryad36/100

Data from: Towards high-resolution modeling of small molecule - ion channel interactions

Ion channels are critical drug targets for a range of pathologies, such as epilepsy, pain, itch, autoimmunity, and cardiac arrhythmias. To develop effective and safe therapeutics, it is necessary to design small molecules with high potency and selectivity for specific ion channel subtypes. There has been increasing implementation of structure-guided drug design for the development of small molecules targeting ion channels. We evaluated the performance of two Rosetta ligand docking methods, RosettaLigand and GALigandDock, on structures of known ligand - cation channel complexes. Ligands were docked to voltage-gated sodium (NaV), voltage-gated calcium (CaV), and transient receptor potential vanilloid (TRPV) channel families. For each test case, RosettaLigand and GALigandDock methods were able to frequently sample a ligand binding pose within 1-2 Å root mean square deviation (RMSD) relative to the experimental ligand coordinates. However, RosettaLigand and GALigandDock scoring functions cannot consistently identify experimental ligand coordinates as top-scoring models. Our study reveals that the proper scoring criteria for RosettaLigand and GALigandDock modeling of ligand - ion channel complexes should be assessed on a case-by-case basis using sufficient ligand and receptor interface sampling, knowledge about state specific interactions of the ion channel and inherent receptor site flexibility that could influence ligand binding.

opencc-zeroMay 2024View details →

Data and scripts (2) for Storkey et al, "Resolution dependence of interlinked Southern Ocean biases in global coupled HadGEM3 models", GMD (2024)

================================================================  Data and scripts for producing plots from Storkey et al (2024):  "Resolution dependence of interlinked Southern Ocean biases in  global coupled HadGEM3 models"  ================================================================ The plots in the paper consist of 10-year mean fields from the third  decade of the spin up and timeseries of scalar quantities for the first 150 years of the spin up. The data to produce these plots are stored in the MEANS_YEARS_21-30 and TIMESERIES_DATA directories respectively. Note that due to the size limit on records on Zenodo, the 10-year mean  output from the N216-ORCA12 integration has been stored as a separate record. Scripts to produce the plots are in SCRIPT, with section definitions in SECTIONS. Bespoke plotting scripts are included in SCRIPT. They use python 3 including the Matplotlib, Iris and Cartopy packages. The  plotting of the timeseries data used the Marine_Val VALSO-VALTRANS  package which is available here:  https://github.com/JMMP-Group/MARINE_VAL/tree/main/VALSO-VALTRANS  Much of the processing of the model output data was performed with the CDFTools package, which is available here:  https://github.com/meom-group/CDFTOOLS and the NCO package:  https://web.mit.edu/course/13/13.715/nco-2.8.1/doc/

opencc-by-4.0Apr 2024View details →

Cellular-resolution X-ray microtomography of an entire mouse brain: supporting data, scripts and parameters

<h2>Abstract </h2> Purpose: Histology is the gold standard for sub-cellular visualization of the mouse brain. It offers excellent in-plane resolution, but a comparably low out-of-plane resolution due to physical sectioning. X-ray microtomography does not require this trade-off. Tomographic imaging of the entire mouse brain with isotropic cellular resolution produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge. Approach: Extended-field X-ray microtomography covering an entire mouse brain was performed. The 4,495 projections from 8 × 8 offset acquisitions were stitched to reconstruct a 15,000^3 voxel volume. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. Results: We present a 3.3 teravoxel dataset covering a full mouse brain with 0.65 μm voxel size. The data were block-wise transformed to a common coordinate system then stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer. Conclusions: This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The data are publicly available and easily accessible for domain experts via browser-based viewers. <h2>Data</h2> File <code>b32_atlas_registration.zip</code> contains the input data, parameter files and output data of affine and non-rigid registration of the 32 x 32 x 32 voxels downsampled microtomography image to the Allen Mouse Brain Common Coordinate Framework v3. File <code>create_sharded_Neuroglacer_format.pdf</code> will provide instructions how to create gZip-compressed, sharded, pre-computed Neuroglancer format via the open source software <a href="https://github.com/seung-lab/igneous">igneous</a>. This is currently still missing. <h2>Processing</h2> Reconstruction of extended field microtomography images mit projection stitching in horizontal and vertical direction was achieved with our software pipeline <a href="https://github.com/unibas-bmc/mosaicreconstruction">mosaicreconstruction</a>. The 32 x  32 x 32 voxels downsampled microtomography image was registered with the open source software <a href="https://elastix.lumc.nl/">elastix (and transformix)</a>. The <code>elastix.log</code> file states the used command line options. Directory names require adapting for reproducing the results.  As terabyte large images and the non-rigid transformation parmeters do not fit into memory, we developed a distributed hierarchical approach with sub-volume transformations for the high resolution level, see <a href="https://github.com/unibas-bmc/LargeVolumeTransformix">LargeVolumeTransformix</a>. The high resolution tomography volume (moving volume) was warped to the atlas (fixed volume) by dividing the fixed space into 12 × 12 × 12 target subregions, such that the axes-aligned extended moving image subregion, the moving image transformed subregion, and the transformation parameters all fit in memory for an isotropic target voxel resolution of 0.65 μm.

dryad36/100

High resolution dataset of plastic deformation at cryogenic temperatures in a nickel-based superalloy

A nickel-based superalloy is examined during monotonic deformation at cryogenic temperatures, reaching as low as liquid helium temperature. A detailed multimodal analysis of the microstructure and plasticity is conducted to discern changes in deformation mechanisms and plastic deformation localization under cryogenic conditions. This study employs high-resolution digital image correlation to identify the deformation mechanisms and understand their influence on plastic deformation localization as the temperature varies. At cryogenic temperatures, unusual plastic deformation localization processes are observed, attributed to the competing activation of a range of deformation processes. Furthermore, a mechanism of slip delocalization, i.e., local plastic deformation homogenization through closely spaced slip, is noted at these extreme temperatures. Ultimately, the impact of the microstructure is identified across the temperature range, from room to cryogenic temperatures.

opencc-zeroMay 2024View details →

Supplementary data to "High-Resolution Raman Imaging of >300 Patient-Derived Cells from Nine Different Leukemia Subtypes: A Global Clustering Approach"

Compressed ".feather" files including the entire dataset of 319 Raman maps of the same number of cells from 19 patients affected by nine distinct leukemia subtypes. Raw data have been pre-processed as follows using custom software (LabVIEW, National Instruments Corp., TX):  a) cosmic rays removal by singular value decomposition (SVD); b) camera offset subtraction; c) CCD response correction (intensity and etaloning) using a tungsten halogen light with known emission (Avalight-HAL, Avantes BV, NL)); d) wavenumber calibration using the zero-wavenumber laser line, toluene and argon-mercury emission (CAL-2000, Ocean Optics, Germany); e) denoising by SVD. More details in the open access published article and supplementary material (10.1021/acs.analchem.4c00787).

Drainage network for a region in central Buenos Aires province, 30m resolution raster, EPSG:5347

This drainage network was obtained using the Copernicus-30 Global Digital-Surface-Model, tiles (S37-38, W60) with QGIS and PCraster plugin: local direction drainage and flow accumulation algorithms. It helps to clarify the surrounding drainage pattern at cities like Azul, Cacharí and Tandil,  for flood alleviation schemes.

opencc-by-4.0Jun 2024View details →

High-resolution topography data and fault trace along the Elashan fault

High-resolution digital elevation models (DEM) topography data extracted from the uncrewed aerial vehicle (UAV) of a DJI (Dajiang Innovations Science and Technology Co., Ltd.) Phantom 4 RTK, and GF-7 satellite stereo imagery. The trace of the Elashan fault is interpreted based on these high-resolution topography data.

Synthetic Emission Line Catalog and High-Resolution SEDs for SPHEREx Galaxy Simulations

Overview: This repository contains the synthetic galaxy models derived from multi-wavelength photometry in the COSMOS field (166k galaxies over 1.27 sq. deg., 18 < i < 25) and from the GAMA survey (44k galaxies over 217 sq. deg., i < 18). These encompass a representative sample of galaxies SPHEREx will observe, and should be applicable for other surveys as well. <ul> <li>Synthetic emission line strengths in the rest-frame optical/near-infrared (H-alpha, H-beta, Paschen-alpha, [OIII], [OII], [NII], [SII])</li> <li>High-resolution SEDs (0.1 - 8 micron), which are produced by 1) fitting a library of 160 galaxy templates to multi-band photometry and 2) inserting emission lines with strengths predicted by an empirical model that depends on galaxy type, redshift and stellar mass.</li> </ul> These products were made using the modeling framework Conditional LIne Painting on Synthetic Spectra (CLIPonSS), the details of which are summarized in Feder+2023b (<a href="https://arxiv.org/abs/2312.04636">arXiv link here</a>). The synthetic emission line catalog is validated against a variety of LF measurements, line ratio trends and direct line comparisons.  Data description: High-resolution SEDs: The SEDs are stored in .FITS files, for which each galaxy SED has its own Header Data Unit (HDU). This format was chosen due to the fact that the wavelength sampling for the 160 galaxy empirical and model-based templates varies, i.e., we do not perform any interpolation onto a homogenized wavelength grid. In cases where emission lines are added but the continuum template resolution is coarse, the resolution is increased in the vicinity of the emission line(s) to adequately sample the line profiles. Each galaxy's HDU is indexed by its Farmer ID (for COSMOS) or alternatively its uberID (GAMA). The COSMOS SEDs are split into three files for relative ease of access, while the GAMA sources are all in one file. Emission line catalogs: The emission line catalogs are stored in .csv format with the following information: Tractor_ID (or uberID) [integer]: Unique identifier for each source RA/DEC [float, in degrees]: Celestial coordinates imag [AB]: i-band magnitude mass_best [float]: log-stellar masses estimated through SED fitting process ebv [float]: Galaxy intrinsic dust extinction (ranging from ebv=0 to 1) redshift [float]: Best-fit redshift from COSMOS2020 (GAMA) catalogs bfit_tid [integer]: Best fit template ID from library of templates dustlaw [integer]: Best fit dust law (1=Prevot, 2=Calzetti, 3=Seaton, 4=Allen, 5=Fitzpatrick) L_{line} [float, erg s-1]: Line luminosities from empirical model F_{line} [float, erg cm-2 s-1]: Line fluxes from empirical model ew_ha [float, Angstrom]: Equivalent width of H-alpha from empirical model Fitting templates: We include the 31 model-based templates and 129 empirical templates from Brown+2014. In the Brown templates we have removed any relevant lines that were directly measured in the initial spectra, however we do not fit for/remove PAH features. These can serve as the basis for other empirically based galaxy simulations with different emission line prescriptions. Any questions regarding the use of these data products or related issues can be directed to Richard Feder (link to <a href="https://richardfeder.github.io/">personal website</a>).