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108 results for “Super-Resolution”
Rapid mapping of flood inundation by deep learning-based image super-resolution
<div> <div># Rapid mapping of flood inundation by deep learning-based image super-resolution</div> <div># Developer: Wenke Song</div> <div># The University of Hong Kong</div> <div># Contact email: songwk@connect.hku.hk</div> <div># MIT License</div> <div># Copyright (c) 2024 songwk0924</div> <div> </div> <div>There are two folders in the compressed file: Trained_model and Test_cases:</div> <div>(1) Trained_model</div> <div> model_d_DenseUnet.pth, for predicting the maximum water depth;</div> <div> model_v_DenseUnet.pth, for predicting the maximum velocity.</div> <div> </div> <div>(2) Test_cases</div> <div> Test_d_r1.npy, Test_d_r2.npy, Test_d_r3.npy: Input features for predicting maximum water depth of rainfall events r1-r3;</div> <div> Test_v_r1.npy, Test_v_r2.npy, Test_v_r3.npy: Input features for predicting maximum velocity of rainfall events r1-r3; <div> </div> </div> <div> bathy_mat_5m_0p.csv: Elevation data to create mask layer;</div> <div> Fine_grid_flood_maps (2DSWEs):</div> <div> hmax_r1.asc, hmax_r2.asc, hmax_r3.asc, maximum water depth simulated by 2DSWEs of rainfall events r1-r3;</div> <div> velmax_r1.asc, velmax_r2.asc, velmax_r3.asc, maximum velocity simulated by 2DSWEs of rainfall events r1-r3;</div> <div> </div> <div><span>The aforementioned data will be used as input for model prediction (Prediction.py). </span></div> <div><a name="OLE_LINK902"></a><a name="OLE_LINK909"></a><a href="https://github.com/songwk0924/Flood-inundation-mapping"><span>https://github.com/songwk0924/Flood-inundation-mapping</span></a></div> </div>
Surrogate Downscaling of Mesoscale Wind Fields Using Ensemble Super-Resolution Convolutional Neural Networks
<p>Datasets and source codes for the manuscript "Surrogate Downscaling of Mesoscale Wind Fields Using Ensemble Super-Resolution Convolutional Neural Networks" submitted to the journal "Artificial Intelligence for the Earth Systems" of the American Meteorological Society.</p>
Supplementary dataset for 'Super-resolution vibrational imaging based on photoswitchable Raman probe'
<p>Here's a dataset for 'Super-resolution vibrational imaging based on photoswitchable Raman probe.' </p>
HEK293T cell super-resolution images by SoRa microscopy
<p>These images contain both untreated and VPA-treated cells, stained by H3K27ac antibodies, CCCTC binding factor (CTCF) antibodies and DNA fluorescent dye Hoechst. Cells were imaged by Yokogawa CSU-W1 SoRa super-resolution spinning disc confocal system (Tokyo, Japan).</p><p>There are two tar.zg files, <a href="https://zenodo.org/uploads/10032412">original_multi-cells_SoRa.tar.gz </a>and <a href="https://zenodo.org/uploads/10032412">single-cells_segmented.tar.gz</a>. "original_multi-cells_Sora.tar.gz" is the original image data, which have multiple cells in each image. On the other hand, "single-cells_segmented.tar.gz" is single-cell image data, obtained from "original_multi-cells_Sora.tar.gz" by segmentation processing.</p>
SUper-Resolution Ultrasound Imaging of Erythrocytes (SURE) in Normal and Malignant Lymph Nodes
ClinicalTrials.gov study NCT05754814. IPD Sharing: UNDECIDED. Countries: 1. Publications: 36.
Clinical Application of Super-resolution Ultrasound(SR-US) Imaging in Solid Tumors
ClinicalTrials.gov study NCT06018142. IPD Sharing: NO. Countries: 1. Publications: 2.
Micro-stepping Extended Focus reduces photobleaching and preserves structured illumination super-resolution features
<p><span>Despite progress made in confocal microscopy, even fast systems still have insufficient temporal resolution for detailed live cell volume imaging, such as tracking rapid movement of membrane vesicles in three-dimensional space. Depending on the shortfall, this may result in undersampling and/or motion artifacts that ultimately limit the quality of the imaging data. By sacrificing the detailed information in the Z-direction, we propose a new imaging modality that involves capturing fast "<i>projections</i>"<i> </i>from the field of depth which shortens imaging time by approximately an order of magnitude as compared to standard volumetric confocal imaging. With faster imaging, radiation exposure to the sample is reduced, resulting in less fluorophore photobleaching and potential photodamage. The implementation minimally requires two synchronized control signals that drive a piezo stage and trigger the camera exposure. The device generating the signals has been tested on spinning disk confocals and instant structured-illumination-microscopy (iSIM) microscopes. Our calibration images show that the approach provides highly repeatable and stable imaging conditions that enable photometric measurements of the acquired data, in both standard live imaging and super-resolution modes. </span></p>
Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
Data from: Depth image super-resolution reconstruction based on a modified joint trilateral filter
Depth image super-resolution (SR) is a technique that utilizes signal processing technology to enhance the resolution of a low-resolution (LR) depth image. Generally, the external database or high-resolution (HR) images are needed for acquiring the priori information to support the SR reconstruction. To overcome the limitation, a depth image SR method which does not need the reference of any external images is proposed. In the paper, a high-quality edge map is firstly constructed using a sparse coding method, which uses a dictionary learned from the original images themselves at different scales. Then, the high-quality edge map is used to guide the interpolation for depth images by a modified joint trilateral filter. During the interpolation, some information of gradient and structural similarity (SSIM) are added to preserve the detailed information and suppress the noise. The proposed method not only can preserve the sharpness of image edge, but also can avoid the dependence on database. Experimental results show the proposed method is superior to some state-of-the-art depth image SR methods.
Data from: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaints probes enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses only molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) and optimized the imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and 29-34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in the human or mouse genome, respectively, demonstrating the capability of MB-based FISH in visualizing a so far shortest and non-repetitive genomic sequence in 3D at super-resolution.
Super-resolution SIM Simulations
<p>Selected sets for SIM super-resolution simulations </p>
live cell super-resolution data_dual_color_cell_line_CTCF_E-2_deletion
Open the record for dataset details and reuse information.
3D drift correction for super-resolution imaging with a single laser light
<p>Original single-molecule image data and analysis results of Figures 4 and 5 in the paper</p>
Data Repository: Fast Single-Particle Tracking of Membrane Proteins Combined with Super-Resolution Imaging of Actin Nanodomains
<p>This repository contains a collection of correlated 2D super-resolution images obtained through single molecule localization microscopy and 3D time series of single particle tracking data of membrane proteins. By utilizing high-speed fluorescent microscopy, we tracked a transmembrane protein – the high-affinity IgE receptor – and an outer-leaflet protein – GPI-anchored protein – at the frame rate of 490 Hz. Subsequently, actin structures of the same cells were captured using a super-resolution microscopy (dSTORM technique). Additionally, this dataset includes Technical Validation to support the transition from live-cell imaging to fixed-cell imaging when adding fixation buffers. </p> <p>The data was classified as “Class I” and “Class II” describing two categories of RBL-2H3 cells. In "Class I", the cells were untransfected. In “Class II”, the cells were transfected to express GFP-GPI-anchored fusion protein. The zip folder names that include “IgE Untreated” include image time series of fluorescently labeled IgE receptors in untreated RBL-2H3 cells and image series of corresponding super-resolution imaging of fluorescently labeled actin filaments of the same cell in “SRImage” folder.</p> <p>The data with folder names including with “IgE Treated” are image time series of fluorescently labeled IgE receptors in either phalloidin- or PMA-treated RBL-2H3 cells and corresponding image series of super-resolution imaging of fluorescently labeled actin filaments in the same cell.</p> <p>Similarly, the data with folder names starting with “GPI Untreated” are image time series of fluorescently labeled GPI-anchored proteins in untreated RBL-2H3 cells and corresponding image series of super-resolution imaging of fluorescently labeled actin filaments in the same cell.</p> <p>The data with folder names starting with “GPI Treated” are image time series of fluorescently labeled GPI-anchored proteins in phalloidin treated RBL-2H3 cells and corresponding image series of super-resolution imaging of fluorescently labeled actin filaments in the same cell.</p> <p>The number within each folder name represents an individual experiment and the corresponding data collected under the same conditions.</p> <p>For all experiments an IR movie was added to monitor the cell morphology during live-cell image and adding initial fixation buffer and it was saved in the tracking file. </p> <p>The HDF5 files of all data are available in the second version of this repository. For each sample, there are two files: "Tracking.h5" and "SuperResolution_actin.h5". The "Tracking" files include two groups: single-particle tracking data and IR images during tracking. The "SuperResolution_actin" files contain two groups: super-resolution images of actin filaments and IR reference images for image registeration and drift correction during data collection. </p> <p> </p> <p> </p> <p> </p>
Dataset related to article Super-resolution study of PIAS SUMO E3-ligases in hippocampal and cortical neurons
<p>Immagini ottenute con la sim e il confocale dei neuroni ippocampali e corticali presenti nelle immagini. Grafici relativi ai coefficenti di localizzazione</p>
Super-resolution microscopy: a brief history and new avenues
<p>A brief history of far-field SRM. (a) Timelines highlighting crucial milestones in the development of SRM techniques (top) and the corresponding introduction of commercial turn-key super-resolution systems (bottom). For each SRM technique, the corresponding authors of the subsequent publication have been listed. (c) The number of publications extracted from the Web of Science database. (d) Correlation between the approximate purchase costs and the nominal lateral (xy) resolution or localization precision (SMLM-based systems) achievable under ideal conditions, for commercial and open-source microscopy systems, respectively.</p>
Super-resolution simultaneous integral imaging with digital refocus in LWIR band
<p>Static and dynamic Super-resolution simultaneous integral imaging with digital refocus in LWIR band</p>
Data for "Scattering-Based Super-Resolution Optical Fluctuation Imaging"
Open the record for dataset details and reuse information.
Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
Dataset of "Super-resolution generative adversarial networks of randomly seeded fields"
<p>Dataset of the article "Super-resolution generative adversarial networks of randomly seeded fields" (https://doi.org/10.1038/s42256-022-00572-7)</p> <p>The codes processing data here are on https://github.com/eaplab/RaSeedGAN</p> <p>This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 949085, NEXTFLOW).</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.