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134 results for “Super resolution”
Data archive for "Stochastic Super-Resolution for Downscaling Time-Evolving Atmospheric Fields with a Generative Adversarial Network"
<p>This datasets supports the paper "Stochastic Super-Resolution for Downscaling Time-Evolving Atmospheric Fields with a Generative Adversarial Network" submitted to IEEE Transactions in Geoscience and Remote Sensing. A preprint of the paper can be found here: <a href="https://arxiv.org/abs/2005.10374">https://arxiv.org/abs/2005.10374</a>. The code that uses these data is available at <a href="https://github.com/jleinonen/downscaling-rnn-gan">https://github.com/jleinonen/downscaling-rnn-gan</a>.</p> <p>The file "goes-samples-2019-128x128.nc" contains the training dataset called "GOES-COT" in the paper, consisting of cloud optical depth measurements from the GOES-16 satellite. The files "gen_weights*.nc" contain the generator weights saved at different time steps during training for the two different datasets described in the paper.<br> </p>
Fast and long-term super-resolution imaging of ER nano-structural dynamics in living cells using a neural network
<p>Datasets acquired and generated for the manuscript "Fast and long-term super-resolution imaging of ER nano-structural dynamics in living cells using a neural network". The datasets include test, training and time series datasets each containing the raw data and the predicted data where it applies. </p>
Dataset T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions
<p>This dataset provides various acquisitions for T2 mapping of the MnCl2 array of the NIST phantom at 1.5T. Data were acquired on a MAGNETOM Sola (Siemens Healthcare, Erlangen, Germany), with an 18-channel body coil and a 32-channel spine coil (12 elements used). It gathers original acquisitions from Lajous H. et al. (2020) T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions. In: Martel A.L. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science, vol 12262. Springer, Cham. https://doi.org/10.1007/978-3-030-59713-9_12.</p> <p>The dataset is composed of DICOM images from:</p> <p>i) Gold-standard single-echo spin echo (SE) sequences acquired at variable TE;</p> <p>ii) Alternative reference multi-echo spin echo (MESE) acquisitions;</p> <p>iii) Half-Fourier Acquisition Single-shot Turbo spin Echo (HASTE) images at variable TE in three orthogonal orientations.</p> <p>The acquisition parameters are further detailed in the ReadMe.txt file provided along with the images.</p> <p>These acquisitions were repeated independently on three different days during the month of January 2020.</p> <p>These data are made publicly available as a support for further reproducibility studies as well as for the validation of new T2 relaxometry strategies.</p> <p>Works using any of these data should cite the following two references:</p> <p>- Lajous H. et al. (2020) T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions. In: Martel A.L. et al. (eds) Medical Image Computing and Computer Assisted Intervention – MICCAI 2020. MICCAI 2020. Lecture Notes in Computer Science, vol 12262. Springer, Cham. https://doi.org/10.1007/978-3-030-59713-9_12</p> <p>- Lajous, Hélène, Ledoux, Jean-Baptiste, Hilbert, Tom, van Heeswijk, Ruud B., & Bach Cuadra, Meritxell. (2020). Dataset T2 Mapping from Super-Resolution-Reconstructed Clinical Fast Spin Echo Magnetic Resonance Acquisitions [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3931812</p>
Super-resolution EO-based area monitoring markers computed over the Lithuanian pilot region (2022)
<p>In the context of the EU-funded project DIONE (No. 870378), the following EO-based monitoring marker maps were released over defined pilot areas over the Lithuanian pilot country, enhanced by features raised from the Super-resolution models. It involved the implementation of matching marking and data fusion deep learning algorithms, which attempt to support the extraction of useful information from highly variable inputs. This will further allow the distinction of landscape features, which would otherwise not be available in initially acquired Sentinel-2 data. The use of VHR data (Copernicus Contributing Missions) in combination with drone imagery will enhance the super-resolution modelling capabilities, enabling the augmentation of the training dataset (spatio-temporal scale) and subsequently leading to increased model performance.<br> The goal was to enhance the outputs of the area monitoring markers and especially in the monitoring of small (i.e. 100m<sup>2</sup>), narrow and elongated parcels. </p> <p>For the needs of DIONE, the aforementioned data were explored and the following area-based monitoring markers were calculated from 01-01-2022 until 01-08-2022 providing tailored information for the needs of the National Paying Agency of Lithuania. </p> <ol> <li> <p><strong>Mowing marker:</strong> used to detect mowing events on meadow/grass like Features Of Interest (FOI)</p> </li> <li> <p><strong>Similarity and distance markers:</strong> used to give additional context to the crop classification and to detect erroneous claims</p> </li> <li> <p><strong>Crop-type marker:</strong> used to detect the specific crop growing on the FOI</p> </li> </ol> <p>This dataset is comprised of one geopackage file, the "S2SR-study-geopackage.gpkg"<em>, which</em> was computed for the Lithuanian pilot region<em>. </em>Descriptions are given below.</p> <p><strong>Super-resolution Markers dataset: </strong>Markers were computed for 16872 FOIs that contain less than 1 Sentinel-2 pixel, using signals from 2022-01-01 until 2022-08-01. </p> <table> <caption><strong>Description of the information contained in the corresponding "Super-Resolution markers" dataset</strong></caption> <thead> <tr> <th scope="col">Attribute name </th> <th scope="col">Description </th> </tr> </thead> <tbody> <tr> <td>CROP_LABEL</td> <td>Reference ID of the polygon </td> </tr> <tr> <td>POLY_ID </td> <td>Declared crop group</td> </tr> <tr> <td>crop_group_prediction_1_classification</td> <td>The FOI label as predicted by the crop group (v2) model</td> </tr> <tr> <td>crop_group_prediction_1_classification_score</td> <td>The pseudoprobability of the crop-group (v1) prediction. A score close to 1 indicates that the model is very confident in the prediction</td> </tr> <tr> <td>crop_group_prediction_2_classification</td> <td>The FOI label as predicted by the crop group (v2) model</td> </tr> <tr> <td>crop_group_prediction_2_classification_score</td> <td>The pseudoprobability of the crop-group (v2) prediction. A score close to 1 indicates that the model is very confident in the prediction</td> </tr> <tr> <td>distance_classification</td> <td>Most similar crops according to the distance marker</td> </tr> <tr> <td>distance_classification_score</td> <td>Distance marker score of a FOI when compared to nearby FOIs with the same claim. A value close to 100 indicates that a FOI is not similar to other FOIs with the same claim.</td> </tr> <tr> <td>mowing_event_count</td> <td>Number of detected mowing events in the observation period</td> </tr> <tr> <td>similarity_classification</td> <td>Most similar crops according to similarity marker</td> </tr> <tr> <td>similarity_classification_score</td> <td>Similarity marker score of a FOI when compared to nearby FOIs with the same claim. A value close to 100 indicates that a FOI is not similar to other FOIs with the same claim</td> </tr> </tbody> </table>
Quantitative comparison of camera technologies for cost-effective Super-resolution Optical Fluctuation Imaging (SOFI) [raw datasets]
<p>Raw datasets accompanying the analysis in "Quantitative comparison of camera technologies for cost-effective Super-resolution Optical Fluctuation Imaging (SOFI)"</p> <p>The datasets contain raw fluorescence microscopy images aimed to be processed in a SOFI analysis. They are acquired with different camera technologies, allowing for direct comparison of an industry-grade CMOS detector with both a scientific-grade sCMOS and emCCD detector.</p>
Terrasar measurement data of "Sar Super-Resolution Using Physics-Aware Adaptive Compressed Sensing"
<p>This data set was used to test of the method described in "Sar Super-Resolution Using Physics-Aware Adaptive Compressed Sensing". It consists of the related Terrasar data and a MATLAB file to import the data into MATLAB.</p>
Dataset: Simulation-based parameter optimization for fetal brain MRI super-resolution reconstruction
<p>This dataset contains the data used in the paper</p> <blockquote> <p>de Dumast, P., Sanchez, T., Lajous, H., Bach Cuadra, M. (2023). Simulation-Based Parameter Optimization for Fetal Brain MRI Super-Resolution Reconstruction. MICCAI 2023. LNCS, vol 14226. Springer, Cham. https://doi.org/10.1007/978-3-031-43990-2_32</p> </blockquote> <p>A preprint can also be found on <a href="https://arxiv.org/abs/2211.14274">arXiv</a>. If you found this dataset useful or used it in your research, please cite this reference.</p> <p>This paper studied the impact of the regularization parameter <span class="math-tex">\(\alpha \)</span> on the super-resolution reconstruction of fetal brain magnetic resonance (MR) images. It used simulated T2-weighted data MR images generated using FaBiAN v2.0, a Fetal Brain magnetic resonance Acquisition Numerical phantom that simulates fast spin echo (FSE) sequences of the developing fetal brain throughout gestation. The dataset contains the raw simulated data, the corresponding ground truths as well as corresponding super-resolution (SR) reconstructions using MIALSRTK and NiftyMIC with varying regularization parameters <span class="math-tex">\(\alpha \)</span>.</p> <p>Copyright (c) - All rights reserved. Medical Image Analysis Laboratory - Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland & CIBM Center for Biomedical Imaging. 2023.</p>
Temporal super-resolution microscopy using a hue-encoded shutter
<p>This dataset contains the data to reproduce the figures in our paper called "Temporal super-resolution microscopy using a hue-encoded shutter", <em>Biomedical Optics Express, 2019</em>.</p> <p>Together with the data, the code is available on <a href="https://github.com/idiap/hesm_distrib">Idiap's GitHub page</a>.</p>
Laser-free super-resolution microscopy
<p>Raw data for "Laser-free super-resolution microscopy"</p> <p>https://www.biorxiv.org/content/10.1101/121061v3.full.pdf</p>
Super-resolution analysis of the origins of the elementary events of ER calcium release in dorsal root ganglion neurons
<p>This is the data supplement for the paper entitled, "Super-resolution analysis of the origins of the elementary events of ER calcium release in dorsal root ganglion neurons"<br><br>There are two principal subdirectories within the enclosed zip file:</p><ol><li>10xEExM_data: The directory contains two exemplar datasets each of 10x Enhanced expansion microscopy images of IP3R1 and RyR immunolabelling in DRG soma, at the sub-plasmalemmal regions.<br> </li><li>Correlative Analysis: The directory contains two sub-directories of worked examples of data and correlative analysis of calcium sparks and dSTORM images of RyR and IP3R. The instructions for the code, run in IDL, are included in the Readme.txt enclosed within.</li></ol>
PROBA-V Super-Resolution dataset
<p>The PROBA-V Super-Resolution dataset is the official dataset of <strong>ESA's Kelvins</strong> <strong>competition for "PROBA-V Super Resolution"</strong>. It contains satellite data from 74 hand-selected regions around the globe at different points in time. The data is composed of radiometrically and geometrically corrected Top-Of-Atmosphere (TOA) reflectances for the RED and NIR spectral bands at <strong>300m</strong> and <strong>100m</strong> resolution in Plate Carrée projection. The <strong>300m</strong> resolution data is delivered as <strong>128x128</strong> grey-scale pixel images, the <strong>100m</strong> resolution data as <strong>384x384</strong> grey-scale pixel images. Additionally, a quality map is provided for each pixel, indicating whether the pixels are concealed (i.e. by clouads, ice, water, missing information, etc.).</p> <p>The goal of the challenge can be described as <strong>Multi-Image Super-resolution</strong>: Construct a single high-resolution image out of a series of more frequent low resolution images.</p> <p>Detailed information about the related competition can be found at <a href="https://kelvins.esa.int/proba-v-super-resolution">https://kelvins.esa.int/proba-v-super-resolution</a>.</p> <p>A publication about the generation of this dataset exists as well: </p> <ul> <li><strong>Märtens M., Izzo D., Krzic A. and Cox D.</strong> "Super-resolution of PROBA-V images using convolutional neural networks." Astrodynamics 3.4 (2019): 387-402. (<a href="https://arxiv.org/pdf/1907.01821.pdf">arxiv version</a>)</li> </ul>
BioSR+: Dataset Extension of biological images for super-resolution microscopy
<p>BioSR+ dataset is an extension of our pre-published BioSR dataset of biological images for super-resolution microscopy, currently including image pairs of low-and-high resolution images of five biology structures (CCPs, ER, MTs, F-actin, Myosin-IIA) and 8 signal levels for each ROI. The BioSR+ dataset is related to our Nature Methods paper "Evaluation and development of deep neural networks for image super-resolution in optical microscopy" (DOI: 10.1038/s41592-020-01048-5) and Nature Biotechnology paper "Rationalized deep learning super-resolution <br> microscopy for sustained live imaging of rapid subcellular processes" (DOI:10.1038/s41587-022-01471-3). Both BioSR and BioSR+ are freely available and can be used for non-commercial purposes with proper citations of above two papers.</p>
Data supporting 3D Super-resolution Optical Fluctuation Imaging with Temporal Focusing with two-photon excitation
<p>Data to support the publication combining temporal focusing two photon excitation with super-resolution optical fluctuation imaging.</p> <div>This research was funded by National Centre of Science, grant number: 2022/47/B/ST7/03465. For the purpose of Open Access, the author has applied a</div> <div>CC-BY public copyright licence to any author Accepted Manuscript (AAM) version arising from this submission</div>
Correlative microscopy of mice cerebellar Purkinje cells from 20x confocal tissue imaging to super-resolution 93x 3D STED of dendritic spines
<p>This Dataset concerns the paper entitled "<em>From tissues to segmentation: a modular framework for multi-scale neuron isolation</em>" by Cauzzo et al. <strong>Nature Comm (2024).</strong></p> <p>S.Cauzzo<sup>$</sup>, E. Bruno, D. Boulet, P. Nazac, M. Basile, A. L. Callara, F. Tozzi, A. Ahluwalia, C. Magliaro, L. Danglot<sup>$</sup><sup>*</sup>, N. Vanello<sup>$</sup><sup>*</sup> *shared senior authorship: Lydia.danglot@inserm.fr ; nicola.vanello@unipi.it</p> <p><sup>$</sup> corresponding authors : cauzzo.simone@gmail.com ; Lydia.danglot@inserm.fr ; nicola.vanello@unipi.it</p> <p> </p>
Source Data and Scripts - MultiMatch: Geometry-Informed Colocalization in Multi-Color Super-Resolution Microscopy
<p>Experimental and simulated STED data and scripts associated with Naas et al. "<em>MultiMatch: Geometry-Informed Colocalization in Multi-Color Super-Resolution Microscopy.</em>" <em>bioRxiv</em> (2024): 2024-02. </p> <p>The MultiMatch Python package and further illustrative examples are available on GitHub repository <a href="https://github.com/gnies/multi_match">https://github.com/gnies/multi_match</a>.</p>
Homogeneous multifocal excitation for high-throughput super-resolution imaging - Expanded centriole particles
<p>Datasets containing the segmented expanded centriole particles. The prefix Hs is used to denote particles acquired in synchronized RPE-1 human cells. Otherwise particles were collected from expanded isolated centrioles from <em>Chlamydomoanas reinhardtii</em>. Resized datasets have uniform voxel size of 14x14x14 nm3 after expansion (56x56x56 nm3 before expansion). Non-resized datasets have 14x14x30 pixel size (56x56x120 nm3 before expansion). All files should be mirrored horizontally/vertically to account for the chirality inversion due to the imaging process</p> <p>The channels in different datasets are:</p> <ul> <li>Chlamy acetylated sample: <ul> <li>C1: acetylated tubulin-Alexa488</li> <li>C2: aTubulin-Alexa568</li> </ul> </li> <li>Chlamy MonoE sample <ul> <li>C1: aTubulin-Alexa488</li> <li>C2: GT335-Alexa568</li> </ul> </li> <li>Chlamy PolyE sample <ul> <li>C1: PolyE-Alexa488</li> <li>C2: aTubulin-Alexa568</li> </ul> </li> <li>Hs sample: <ul> <li>C1: PolyE-Alexa488</li> <li>C2: acetylated tubulin-Alexa586</li> </ul> </li> </ul>
Implementation of a 4Pi-SMS super-resolution microscope - Example data II
<p>4Pi-SMS image of Nup96-SNAP labelled with BG-Alexa 647 in the lower nuclear envelope of a U2OS cell in TDE-based index-matching imaging buffer</p>
DeepBedMap: A super-resolution neural network created bed topography of Antarctica
<p>Going beyond BEDMAP2 using a super resolution deep neural network.</p> <p>deepbedmap_v1.1.0.zip: Python code for the DeepBedMap Super-Resolution Generative Adversarial Network.</p> <p>deepbedmap_dem.tif: Digital Elevation Model (250 m spatial resolution) in GeoTiff format, using Antarctic Polar Stereographic Projection (EPSG:3031).</p> <p>srgan_generator_model_weights.npz: The Generator neural network weights/parameters as a NumPy zip file.</p> <p> </p>
BioTISR: a time-lapse biological image dataset for super-resolution microscopy
<p>BioTISR is a biological image dataset for super-resolution microscopy, currently including 2D and 3D time-lapse image pairs of low-and-high resolution images of a variety of biology structures, aiming to provide a high-quality dataset of time-lapse biological SR images for the community to spark more developments of computational SR methods.</p> <p>At present, 2D dataset includes five specimens (clathrin-coated pits, lysosomes, outer mitochondrial membrane, microtubules, and F-actin) acquired with the GI/TIRF-SIM mode and nonlinear SIM mode of our Multi-SIM system, and 3D dataset includes three specimens (outer mitochondrial membrane, microtubules, and F-actin) acquired with 3D-SIM mode of the Multi-SIM system. For each type of specimen and each imaging modality, we acquired the raw data from at least 50 distinct regions-of-interest (ROI). For each ROI, we acquired two (3D data) or three (2D data) groups of N-phase × M-orientation × T-timepoint raw images with a constant exposure time but increasing the excitation light intensity, where (N, M, T) are (3, 3, 20) for TIRF-SIM and GI-SIM, (5, 5, 10) for nonlinear SIM, and (3, 5, 10) for 3D-SIM. Specific imaging conditions and scripts for reading MRC file are provided in Supplement Files.</p> <p>The BioTISR dataset is related to the following paper:<a href="https://www.nature.com/articles/s41587-025-02553-8#citeas">Qiao, C., Liu, S., Wang, Y. <em>et al.</em> A neural network for long-term super-resolution imaging of live cells with reliable confidence quantification. <em>Nat Biotechnol</em> (2025). https://doi.org/10.1038/s41587-025-02553-8</a>, which is an extension of our previously published <a href="https://doi.org/10.6084/m9.figshare.13264793.v9">BioSR dataset</a> (https://www.nature.com/articles/s41592-020-01048-5).</p> <p>Limited by quota, the original images uploaded in the current 3D dataset are wide-field images obtained after averaging 15 images, where (N, M, T) are (1, 1, 10). We will update them to raw SIM images after the quota is expanded.</p> <p>2D dataset's url:</p> <p><a href="https://doi.org/10.5281/zenodo.13843670" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13843670</a></p> <p>3D dataset's urls:</p> <p>F-actin:</p> <p>WF input: <a href="https://doi.org/10.5281/zenodo.13843673">https://doi.org/10.5281/zenodo.13843673</a></p> <p>Raw SIM input:<a href="https://doi.org/10.5281/zenodo.13994464" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13994464</a></p> <p>Microtubules:</p> <p>WF input: <a href="https://doi.org/10.5281/zenodo.13932988" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13932988</a></p> <p>Raw SIM input: <a href="https://doi.org/10.5281/zenodo.13989327" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13989327</a></p> <p>Mitochondria:</p> <p>WF input: <a href="https://doi.org/10.5281/zenodo.13843183" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13843183</a></p> <p>Raw SIM input: <a href="https://doi.org/10.5281/zenodo.14000502" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.14000502</a></p> <p> </p> <p>Update 2025.5.6</p> <p>Add optical transfer function(OTF) of the microscopy system and the pixel size of each data to the supplementary files.</p>
Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body
<p>Data associated with the article "Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body". A README.txt is provided that explains the data provided.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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International Brain Laboratory public data
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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.