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134 results for “Super Resolution”
Data from: Cholesterol and ORP1L dependent clustering of dynein on endolysosmes in cells 2 revealed by super resolution microscopy
<p>The sub-cellular positioning of endolysosomes is crucial for regulating their function. Particularly, the positioning of endolysosomes between the cell periphery versus the peri-nuclear region impacts autophagy, mTOR (mechanistic target of rapamycin) signaling and other processes. The mechanisms that regulate the positioning of endolysosomes at these two locations are still being uncovered. Here, using quantitative super-resolution microscopy in intact cells, we show that the retrograde motor dynein forms nano-clusters on endolysosomal membranes containing 1-2 dyneins, with an average of ~3 nanoclusters per endolysosome. These data suggest that a very small number of dynein motors (1-6) drive endolysosome motility inside cells. Surprisingly, dynein nano-clusters are slightly larger on peripheral endolysosomes having higher cholesterol levels compared to peri-nuclear ones. By perturbing endolysosomal membrane cholesterol levels, we show that dynein copy number within nano-clusters is influenced by the amount of endolysosomal cholesterol while the total number of nano-clusters per endolysosome is independent of cholesterol. Finally, we show that the dynein adapter protein ORP1L (Oxysterol Binding Protein Homologue) regulates the number of dynein motors within nano-clusters in response to cholesterol levels. We propose a new model by which endolysosomal transport and positioning is influenced by the cholesterol sensing adapter protein ORP1L, which influences dynein's copy number within nano-clusters.</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
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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 ET: actual and downscaled
<p>Super Resolution ET: actual and downscaled</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"
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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>
Supplement to the manuscript "Overcoming computational challenges to realize meter-to-submeter-scale resolution in cloud simulations using super-droplet method" (Matsushima et al., 2023)
<p>Supplemental codes, figures, movies, and datasets to the manuscript "Overcoming computational challenges to realize meter-to-submeter-scale resolution in cloud simulations using super-droplet method" (Matsushima et al., 2023)</p> <p>See README.md for more details.</p>
Data from: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes
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Data from: Depth image super-resolution reconstruction based on a modified joint trilateral filter
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
Open the record for dataset details and reuse information.
Data from: Cholesterol and ORP1L dependent clustering of dynein on endolysosmes in cells 2 revealed by super resolution microscopy
Open the record for dataset details and reuse information.
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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.