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108 results for “Super-Resolution”
Dataset for Reference-free Isotropic Super-resolution For Volumetric Fluorescence Microscopy
<p>Dataset for a research paper titled "Deep learning enables reference-free isotropic super-resolution for volumetric fluorescence microscopy". The images were acquired using two modalities: confocal fluorescence microscopy (CFM) and open-top light-sheet microscopy (OT-LSM). For details about the imaging, please refer to the paper (Link to be uploaded later). </p> <p>A. CFM</p> <ul> <li>CFM image of a cortical region of a Thy 1-eYFP mouse brain. </li> <li>Lateral resolution estimated as 1.24 micron and Z-depth interval of 3 micron</li> </ul> <ol> <li>Input image ["CFM_input_xy-view.tif] [Figure 2] </li> <li>Reference image acquired by rotating the sample by 90 degrees ["CFM_rotated-and-registered_xz-view.tif'] [Figure 2] </li> </ol> <p>B. OT-LSM </p> <ul> <li>OT-LSM image of a cortical region of a Thy 1-eYFP mouse brain.</li> <li>Lateral resolution estimated as 0.5 micron and axial resolution estimated as 4.6 micron. </li> <li>For testing of artifact correction, the microscope was poorly calibrated on purpose. </li> </ul> <ol> <li>Input image for artifact correction ["OT-LSM_artifact-correction_input_volume_xy-view.tif"] [Figure 4]</li> <li>Ground-truth image for artificial blurring ["OT-LSM_artificial-blurring_GT.tif"][Supplementary Figure 14]</li> <li>Input image for artificial blurring ["OT-LSM_artificial-blurring_gau-z-blurred-std-10.tif"][Supplementary Figure 14]</li> <li>Input image for PSF deconvolution ["input_volume_PSF-deconvolution.tif"][Figure 3]</li> </ol> <p>C. Simulation </p> <ul> <li>Jupyter notebook to generate a 3D image volume for simulation ["Data Generator for Simulation.ipynb"] [Figure 1] </li> </ul>
Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element
<p>Raw data for the article "Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element". Each set of three files is a set of dSTORM images, taken using either top-hat illumination or a Gaussian illumination. For Sample 0, the top-hat illumination was performed first. For Sample 1, the Gaussian illumination was performed first.</p>
Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines
<p>This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "<em>From tissues to segmentation: a modular framework for multi-scale neuron isolation</em>" by Cauzzo et al. <strong>Nature Comm (2024).</strong></p>
Fully-Automated Multicolour Structured Illumination Module for Super-resolution Microscopy
<p> </p> <p>In the rapidly advancing field of biological imaging, high-resolution techniques that are cost-effective and accessible are essential for observing and understanding intracellular dynamics. Structured illumination microscopy (SIM) is a preferred method for achieving high axial and lateral resolution in living samples due to its optical sectioning and minimal phototoxicity. However, the high cost and complexity of conventional SIM systems limit their widespread use. In our work, we present an open-source, fully-automated, two-color structured illumination module that is compatible with commercially available microscope stands. The compact design, which includes low-cost single-mode fiber-coupled lasers and a digital micromirror device (DMD), is integrated into the open-source acquisition and control software ImSwitch to facilitate real-time super-resolution imaging. This system achieves up to a 1.55-fold improvement in lateral resolution compared to conventional wide-field microscopy. </p> <p>To ensure optimal DMD diffraction performance, we developed a model using tilt and roll pixels, enabling the use of low-cost video projectors in coherent SIM setups. Our aim is to democratize SIM-based super-resolution microscopy by providing comprehensive open-source documentation and a modular software framework compatible with various hardware components (e.g., cameras, stages) and reconstruction algorithms. </p> <p>All datasets generated and analyzed during this study are openly available and can be accessed through our public repository <a href="https://opensimmo.github.io/">[repository link]</a>. The datasets include raw and processed images, calibration files, and software scripts, enabling replication and further innovation. This approach will help upgrade as many devices as possible to the super-resolution realm, fostering greater accessibility and collaboration in the scientific community</p>
3D super-resolution datasets associated with the paper "Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet"
<p>3D single-molecule super-resolution datasets corresponding to reconstructions shown in <em>Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet</em> by Saliba & Gagliano, Gustavsson et. al.</p>
RELLISUR: A Real Low-Light Image Super-Resolution Dataset
<p>The RELLISUR dataset contains real low-light low-resolution images paired with normal-light high-resolution reference image counterparts. This dataset aims to fill the gap between low-light image enhancement and low-resolution image enhancement (Super-Resolution (SR)) which is currently only being addressed separately in the literature, even though the visibility of real-world images is often limited by both low-light and low-resolution. The dataset contains 12750 paired images of different resolutions and degrees of low-light illumination, to facilitate learning of deep-learning based models that can perform a direct mapping from degraded images with low visibility to high-quality detail rich images of high resolution. The associated paper can be found here: <a title="https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/file/7ef605fc8dba5425d6965fbd4c8fbe1f-Paper-round2.pdf" href="https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/file/7ef605fc8dba5425d6965fbd4c8fbe1f-Paper-round2.pdf" target="_blank" rel="noopener">https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/file/7ef605fc8dba5425d6965fbd4c8fbe1f-Paper-round2.pdf</a></p>
Wood Buffalo Environmental Association (WBEA) Historical Monitoring Data used in "Passive Tracer Modelling at Super-Resolution with WRF-ARW to Assess Mass-Balance Schemes"
<p>Wood Buffalo Environmental Association (WBEA) Historical Monitoring Data from two monitoring stations Bertha Ganter – Fort McKay and Barge Landing for 20 August 2013 to 2 September 2013. This data was used in "Passive Tracer Modelling at Super-Resolution with WRF-ARW to Assess Mass-Balance Schemes" (Fathi et al., 2022 - egusphere-2022-1125) for model output and observational data comparisons. The same data can be accessed and downloaded from "<a href="https://wbea.org/historical-monitoring-data/">https://wbea.org/historical-monitoring-data/</a>".</p>
An Agnostic Benchmark for Optical Remote Sensing Image Super-Resolution
<p>In remote sensing, image super-resolution (ISR) is a technique used to create high-resolution (HR) images from low-resolution (R) satellite images, giving a more detailed view of the Earth’s surface. However, with the constant development and introduction of new ISR algorithms, it can be challenging to stay updated on the latest advancements and evaluate their performance objectively. To address this issue, we introduce SRcheck, a Python package that provides an easy-to-use interface for comparing and benchmarking various ISR methods. SRcheck includes a range of datasets that consist of high-resolution and low-resolution image pairs, as well as a set of quantitative metrics for evaluating the performance of SISR algorithms.</p>
CBRA: The first multi-annual (2016-2021) and high-resolution (2.5 m) building rooftop area dataset in China derived with Super-resolution Segmentation from Sentinel-2 imagery
<p>Large-scale and up-to-date maps of building rooftop area (BRA) are crucial for addressing policy decisions and sustainable development. In addition, as a fine-grained indicator of human activities, BRA could contribute to urban planning and energy modeling to provide benefits to human well-being. However, existing large-scale BRA datasets, such as those from Microsoft and Google, do not include China, hence there are no full-coverage maps of BRA in China. To this end, we produce the multi-annual China building rooftop area dataset (CBRA) with 2.5 m resolution from 2016-2021 Sentinel-2 images. The CBRA is the first full-coverage and multi-annual BRA data in China. The CBRA achieves good performance with the F1 score of 62.55% (+10.61% compared with the previous BRA data in China) based on 250,000 testing samples in urban areas, and the recall of 78.94% based on 30,000 testing samples in rural areas. </p> <p>The CBRA is organized as GeoTIFF (.tif) raster file format with a single band and GCS_WGS_1984 coordinate system. The pixel values are 0 and 255, with 0 representing the background and 255 representing the building rooftop area. Furthermore, to facilitate the use of the data, the CBRA is split into 215 tiles of spatial grid, named “CBRA_year_E/W**N/S**.tif”, where “year” is the sampling year, the “E/W**N/S**” is the latitude and longitude coordinates found in the upper left corner of the tile data.</p> <p> </p> <p>Version 2.0: In version 1.0, there were empty raster images (because they didn't contain buildings). In version 2.0, these raster images were removed.</p>
Multi-colour super-resolution images of untreated and rifampicin-treated Xenorhabdus doucetiae (LB, exponential phase)
<p> This dataset and CARE model is part of the publication "<strong>Transertion and cell geometry organize the </strong><i><strong>Escherichia coli</strong></i><strong> nucleoid during rapid growth</strong>".</p><p>It contains all SMLM images that were used for the publication, as well as the single-cell regions of interest for analyses.</p><p>Xenorhabdus doucetiae chromosomally expressing MreBsw-sfGFP were grown to exponential phase in LB Lennox and antibiotics were added for 0-30 min. Cultures were then chemically fixed, permeabilised and imaged for the nucleoid (JF646-Hoechst) and membranes (Nile Red) using PAINT.</p><p>More information can be found in the publication.</p>
Comparing Lifeact and Phalloidin for super-resolution imaging of actin in fixed cells
<p>Visualizing actin filaments in fixed cells is of great interest for a variety of topics in cell biology such as cell division, cell movement, and cell signaling. We investigated the possibility of replacing phalloidin, the standard reagent for super-resolution imaging of F-actin in fixed cells, with the actin binding peptide `lifeact'. We compared the labels for use in single molecule based super-resolution microscopy, where AlexaFluor 647 labeled phalloidin was used in a (d)STORM modality and Atto 655 labeled lifeact was used in a single molecule imaging, reversible binding modality. We found that imaging with lifeact had a comparable resolution in reconstructed images and provided several advantages over phalloidin including lower costs, the ability to image multiple regions of interest on a coverslip without degradation, simplified sequential super-resolution imaging, and more continuous labeling of thin filaments.</p>
Corrected super-resolution microscopy enables nanoscale imaging of auto-fluorescent lung macrophages
<p>Observing the cell surface and underlying cytoskeleton at nanoscale resolution using super-resolution microscopy has enabled many insights into cell signalling and function. However, the nanoscale dynamics of tissue-specific immune cells have been relatively little studied. Tissue macrophages, for example, are highly auto-fluorescent, severely limiting the utility of light microscopy. Here, we report a correction technique to remove auto-fluorescent noise from Stochastic Optical Reconstruction Microscopy (STORM) datasets. Simulations identified a moving median filter as an accurate and robust correction technique. Using this, we were able to visualise lung macrophages activated through Fc receptors by antibody-coated glass slides. Accurate, nanoscale quantification of macrophage morphology revealed that activation induced the formation of cellular protrusions tipped with MHC class I protein. These data are consistent with a role for lung macrophage protrusions in antigen presentation. We further show that the tetraspanin and extracellular vesicle (EV) marker CD81 appears in ring-shaped structures (mean diameter 93 ± 50 nm) at the surface of activated lung macrophages, likely marking the secretion of extracellular vesicles. Moreover, this correction method for super-resolution microscopy is widely applicable to other challenging biological samples.</p>
Data from: Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy
<p>This repository contains the raw data of the experimental ISM dataset used to make the figures and supplementary figures for the paper entitled <em>Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy.<br></em></p>
Dataset for Super-Resolution Image Reconstruction based on Random-coupled Neural Network and EDSR
<p>This dataset folder contains the DIV2K public dataset, which is utilized for model training and comprises 900 high-quality, high-resolution images along with their corresponding low-resolution versions. Additionally, all pre-trained models used in the experiment and their associated test results are publicly available.</p> <p>The main directory is organized into two subfolders: one labeled "dataset," which houses the DIV2K dataset, and another named "Model_results," which contains the pre-trained models and their corresponding test outcomes. The Dataset folder includes the original DIV2K dataset (referred to as "DIV2K") as well as a channel-expanded dataset processed by the RCNN model (designated as "DIV2K-RCNN"). Within the Model_results folder, the Model_trained subfolder contains all pre-trained models employed during the experiment, while the Test_results subfolder holds the test results for each model.</p>
Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging
<p>Data associated with publication.</p>
Long-wave infrared super-resolution wide-field microscopy by sum-frequency generation - experimental data
<p>Experimental Data for "Long-wave infrared super-resolution wide-field microscopy by sum-frequency generation", under consideration at APL, preprint: <a href="https://doi.org/10.48550/arXiv.2112.08112">https://doi.org/10.48550/arXiv.2112.08112</a></p> <p>Files:</p> <p>readme.txt: explanation of the content<br> SFGmicroscope.h5: microscope data<br> APL_test_script.m: matlab test script generating the relevant figures from the data</p> <p>For more information, please contact Richarda Niemann (niemann@fhi-berlin.mpg.de) or Alex Paarmann (alexander.paarmann@fhi-berlin.mpg.de).</p>
Remote Sensing Satellite Video Dataset for Super-resolution
<p>This is a satellite video super-resolution dataset generated from "Jilin-1" video satellite.</p> <p>Training set: 189 clips; Test set: 12 clips.</p> <p>More details can be found in our paper published in IEEE TGRS: https://ieeexplore.ieee.org/document/9530280</p> <p>If you find our work helpful, please cite our paper. Thank you very much!</p>
BreizhSR: multi-temporal cross-sensor super-resolution of satellite imagery
<h1>BreizhSR, a super-resolution Sentinel-2 to SPOT-6/7 dataset </h1> <h2>1. Dataset motivation</h2> <p><strong>BreizhSR</strong> is a dataset targetting super-resolution of (RGB bands of) Sentinel-2 images by providing time series colocated in space and time with SPOT-6/7 acquisitions. This dataset is composed of cloud free Sentinel-2 time series (visible bands at 10m resolution) and SPOT-6/7 pansharpened color images resampled 2.5m resolution. The study area is the region of Brittany (Breizh in the local language), located on the northwestern coast of France with an oceanic climate. The dataset covers about 35 000 km² with mostly agricultural areas (about 80 %). All acquisitions are from 2018 in the Brittany region of France.</p> <h2>2. Dataset organization</h2> <p>The dataset folder follows the structure detailed below :</p> <p><code>BreizhSR</code><br><code>├── dataset_test.pkl</code><br><code>├── dataset_train.pkl</code><br><code>├── README.md</code><br><code>├── x</code><br><code>├── x_test</code><br><code>├── y</code><br><code>└── y_test</code></p> <p>The <code>README.md</code> file contains the same information as this description.</p> <p>Actual image patches are stored in the <code>x</code> and <code>x_test</code> folders for Sentinel-2 patches, and in the <code>y</code> and <code>y_test</code> folders for ground truth SPOT patches. Subfolders are organized using a integer identifier (e.g. <code>8355</code>) that denote the series identifier. Therefore, for the S2 series <code>x/8355</code>, the corresponding SPOT patch is in subfolder <code>y/8355</code>.</p> <p>This organization and additional metadata are described in two <a href="https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.html">Pandas Dataframes</a> : <code>dataset_train.pkl</code> and <code>dataset_test.pkl</code>. These files are Dataframes serialized using the <a href="https://docs.python.org/3/library/pickle.html">pickle Python serialization protocol</a>. The columns available in these Dataframes are described in the table below.</p> <table> <tbody> <tr> <td>x</td> <td>y</td> <td>wkt</td> <td>spot6_name</td> <td>sen2_acquisitions</td> <td>dates_sen2</td> <td>dates_spot6</td> <td>split</td> </tr> <tr> <td>Latitude of the center point (expressed in Lambert 93 CRS)</td> <td>Longitude of the center point (expressed in Lambert 93 CRS)</td> <td>Area of interest geometry in well-known text format</td> <td>Path to the SPOT ground truth</td> <td>Paths to the Sentinel-2 input series</td> <td>Acquisition dates for the Sentinel-2 images</td> <td>Acquisition date for the SPOT ground truth</td> <td>`train` or `test`</td> </tr> </tbody> </table> <h2>3. Data collection and preprocessing</h2> <h3>Sentinel-2</h3> <p>Sentinel-2 constellation has twin satellites launched by the European Space Agency (ESA) in 2015 and 2017 that cover all Earth’s surfaces every five days at the equator. Level-2A images of the BreizhSR dataset are gathered via the THEIA platform, which employs the MAJA pre-processing algorithm to obtain atmospherically corrected ground reflectance. To match the SPOT-6 spectral characteristics, only RGB bands at a 10-meter spatial resolution (B4, B3,and B2) are used in the analysis. The images were collected for the nine tiles covering the Brittany region from the 1st of April 2018 to the 31st of August 2018, filtering images with a cloud cover under 5 %. Since the SPOT-6 data was acquired in the summer of 2018, the Sentinel-2 time period was chosen to include images from before and after the SPOT-6 acquisitions while staying in a range of similar seasonal and climate conditions.</p> <p>Sentinel-2 tiles are cropped into 3x74x74 patches. The dataset is preprocessed with a min-max normalization, using the 2% and 98% percentile as an estimation of minimum and maximum values of Sentinel-2 data to take into account the presence of outliers due to artifacts such as clouds and their shadows.</p> <h3>SPOT-6/7</h3> <p>Orthorectified SPOT data under the Licence Ouverte is collected from the <a href="https://openspot-dinamis.data-terra.org/">DINAMIS</a> platform. Multispectral images at 6m resolution are pansharpened using the panchromatic 1.5m reference using the RCS algorithm <a href="https://www.orfeo-toolbox.org/CookBook/Applications/app_BundleToPerfectSensor.html">Orfeo ToolBox</a>, similar to the Brovey pansharpening algorithm. The pansharpened tiles are preprocessed with a min-max normalization, downsampled at 2.5m resolution and patches are finally cropped with dimensions 3x296x296.</p> <h2>4. License</h2> <p>SPOT images and the Sentinel-2 Theia L2A products are released under the <a href="https://www.etalab.gouv.fr/wp-content/uploads/2018/11/open-licence.pdf">Licence Ouverte 2.0</a> from the French government. This dataset contains modified Coprnicus Sentinel data from 2018, made available under free access by EU law. Other files in the dataset are licensed under Creative Commons Attribution 4.0 (CC BY 4.0).</p> <h3>Acknowledgements</h3> <p>We thank the support of GDR IASIS for funding this work under the SESURE project, the DINAMIS consortium, CNES/Airbus and IGN for access to the SPOT-6 data, and ESA for access to Sentinel-2 data. During the conduct of this research, Simon Donike received a European scholarship to engage in Master Copernicus in Digital Earth, Erasmus Mundus Joint Master Degree (EMJMD). We thank Dirk Tiede (Uni. Salzburg) for his help and feedback on BreizhSR. This work was performed using HPC resources from GENCI–IDRIS (grant 2022-AD011013003).</p>
Advances in volumetric super-resolution microscopy and single-particle tracking (associated codes and datasets)
<h2>Overview</h2> <p>This Zenodo repository contains datasets and code relating to the thesis entitled "Advances in volumetric super-resolution microscopy and single-particle tracking" by <a href="https://www.ch.cam.ac.uk/person/sgd46">Sam G. Daly</a> (Yusuf Hamied Department of Chemistry, University of Cambridge).</p> <p>Managed/updated versions my be avalible at <a href="https://github.com/TheLeeLab">https://github.com/TheLeeLab</a>.</p> <p>The Excel Workbook 'MicrolensRelayCalculator' is designed to help in the design of MLAs for SMLFM.</p> <h2>Available Datasets</h2> <h3>Chapter 4</h3> <ol> <li>Simulated localisation data for various PSFs: standard, astigmatism, double helix, SMLFM, and tetrapod; 4000 detected photons, 20 emitters per frame, 200 frames.</li> <li>Microtubule imaging in a fixed HeLa cell (dSTORM); 30 ms exposure, 640 nm excitation, 200 frames.</li> </ol> <h3>Chapter 5</h3> <ol> <li>B cell receptor imaging on a fixed B cell (dSTORM);<em> 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.</em></li> <li>SPT of the B cell receptor on a live B cell (PALM); <em>20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.</em></li> <li>Membrane imaging on a fixed Jurkat T cell embedded in agarose (resPAINT); <em>20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.</em></li> <li>PD-1 imaging on a fixed T cell (dSTORM);<em> 30 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.</em></li> <li>Membrane imaging on a fixed T cell (resPAINT); <em>20 ms exposure, 640 nm excitation, 200 frames, fiducial: nanodiamonds.</em></li> </ol> <h3>Chapter 6</h3> <ol> <li>SPT of ACBD3 in a live HeLa cell (PALM); <em>20 ms exposure, 640 and 405 nm excitation, 200 frames.</em></li> <li>SPT of TMD mutant (length: 27) in a live HeLa cell (PALM); <em>20 ms exposure, 640 and 405 nm excitation, 200 frames.</em></li> </ol> <h2>Available Code</h2> <ol> <li><strong>Autofocus (BeanShell):</strong> Counteracts axial drift in SMLFM experiments.</li> <li><strong>Calibration (BeanShell):</strong> Controls the piezo scanner for axial calibrations in 3D-SMLM.</li> <li><strong>3D Reconstruction (Matlab):</strong> Reconstructs 2D-localised SMLFM data in 3D. Maintained version available on GitHub.</li> <li><strong>Fiducial correction (Matlab):</strong> Removes focal drift artifacts from 3D localisation data.</li> <li><strong>Temporal grouping (Python):</strong> Removes multiple single-molecule blinking events.</li> <li><strong>3D tracking (Matlab):</strong> Converts 3D localisations into tracks and calculates diffusion quantities.</li> <li><strong>Matching (Matlab):</strong> Determines PPV, sensitivity, and Jaccard index from localisation data.</li> <li><strong>Membrane curvature (Python):</strong> Determines the frequency of 3D localisations at a given membrane curvature.</li> </ol> <h3><em>Supported by The Royal Society (RGF\EA\181021) </em></h3>
DRET-DNA PAINT: using Dark dyes for fast super-resolution imaging
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