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18 results for “live-cell imaging”
Live-cell STED dataset of mitochondria containing ground truth and corresponding low intensity noisy images
<p>The dataset was acquired as part of the manuscript "Denoising diffusion models for high-resolution microscopy image restoration". The dataset contains ground truth and low intensity STED images of mitochondria acquired in live U2-OS cells stably expressing TOM20 coupled to the dead mutant of HaloTag7 which was made fluorescent by using the exchangeable ligand Hy4 bound to the fluorophore SiR. </p>
Subcellular behavior model enables highly precise temporal super-resolved live-cell imaging
<div> <div>This repository contains the preprocessed dataset for [SuB-VFI](https://github.com/sduzzx857/SuB-VFI), including the real datasets we collected and the simulated testing and training datasets. You can refer to the Github repository for details.</div> <div> </div> <div>The simulated testing datasets can be downloaded from [the 2014 ISBI Particle Tracking Challenge](http://bioimageanalysis.org/track/).</div> <div>The EB1 datasets can be downloaded from the paper [The dynamic behavior of the APC-binding protein EB1 on the distal ends of microtubules](https://www.cell.com/current-biology/fulltext/S0960-9822(00)00600-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS096098220000600X%3Fshowall%3Dtrue). We used *Movie2* from the Supplementary data.</div> <br> <div>The CCR5 datasets can be downloaded from the paper [Tracking receptor motions at the plasma membrane reveals distinct effects of ligands on CCR5 dynamics depending on its dimerization status](https://elifesciences.org/articles/76281). We used *Video4* in the Results section. </div> <div> </div> <div>The Lysosome datasets can be downloaded from [Content-Aware Frame Interpolation Microscopy Datasets](https://zenodo.org/records/10076346). We used data from the `Zproject` folder within the compressed file `Source_Data_Lysosomes_z-proj_Fig_5.zip`</div> </div>
Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging
<p><strong>Overview</strong></p> <p>This repository contains all the raw and processed trajectory data associated with “paper title”. In this ReadMe file we provide the following information:</p> <ul> <li>The cell lines and conditions used in this study</li> <li>A summary of how the data was collected</li> <li>The structure of the chromosome locus tracking data</li> </ul> <p><strong>Cell lines and conditions</strong></p> <p>In total, the dataset covers 12 experimental conditions representing the following cell lines and treatment conditions:</p> <ul> <li>C36</li> <li>C65</li> <li>C27</li> <li>CTCF-AID (untreated)</li> <li>CTCF-AID (2 hours AID)</li> <li>CTCF-AID (4 hours AID)</li> <li>RAD21-AID (untreated)</li> <li>RAD21-AID (2 hours AID)</li> <li>RAD21-AID (4 hours AID)</li> <li>WAPL-AID (untreated)</li> <li>WAPL-AID (4 hours AID)</li> <li>WAPL-AID (6 hours AID)</li> </ul> <p> </p> <p><strong>Data and data processing</strong></p> <p>Trajectories were obtained from 3D timeseries of mouse embryonic stem cell colonies in the conditions listed above using a LSM900 Airyscan 2 Zeiss microscope. For each movie we recorded 365 frames of 49.69 µm x 49.69 µm (584 x 584 pixels, pixel size: 0.085 µm by 0.085 µm), separated by an interval of 20 seconds for a total of just over 2 hours. 3D images were composed of 30 z-stacks separated by 0.25 µm, for a total height of 7.25 µm. Imaging was performed in two colors allowing the tracking of two arrays of fluorophores on Chromosome 18 near the <em>Fbn2</em> gene. In all conditions, the fluorophore arrays were separated by 515 kb (except the C27 clone where separation was 10 kb).</p> <p>The 3D image time series were processed using ConnectTheDots: <a href="https://github.com/ahansenlab/connect_the_dots">https://github.com/ahansenlab/connect_the_dots</a> to obtain paired trajectories of chromosome loci over time. The trajectories have been corrected for chromatic shifts and aberrations.</p> <p>Data are provided in an “unfiltered” format (meaning that individual dot localizations were not quality control filtered) , or a filtered format (the same data set, but having undergone quality control). The filtered (quality controlled) trajectory data was used for all the quantitative analyses in the article “”.</p> <p>File names are formatted follows.</p> <ul> <li>Quality controlled data have the structure: {Clone_and_condition_name}.tagged_set.tsv</li> <li>Unfiltered data have the structure: {Clone_and_condition_name}.unfiltered.tagged_set.tsv</li> </ul> <p>For example, for RAD21-AID tagged clone, for imaging performed after two hours of protein degradation, the quality-controlled file name is: RAD21_2_hr.tagged_set.tsv. Please note that for all no-treatment conditions, we used “0 hours” as the tag. Thus, the RAD21 (untreated) becomes RAD21_0_hr.tagged_set.tsv.</p> <p> </p> <p><strong>Structure of Data</strong></p> <p>The trajectory data are provided as tab-separated text files consisting of 10 columns. The column headers are:</p> <ul> <li>id: a unique dot pair index</li> <li>t: the frame in which the dots were localized</li> <li>x: x-coordinate of the dot in the EGFP channel (units in µm)</li> <li>y: y-coordinate of the dot in the EGFP channel (units in µm)</li> <li>z: z-coordinate of the dot in the EGFP channel (units in µm)</li> <li>x2: x-coordinate of the dot in the mScarlet channel (units in µm)</li> <li>y2: y-coordinate of the dot in the mScarlet channel (units in µm)</li> <li>z2: z-coordinate of the dot in the mScarlet channel (units in µm)</li> <li>dist: 3D distance between the dots across channels (units in µm)</li> <li>movie_index: an identifier used to link the dot pair back to the raw image timeseries.</li> </ul>
Live-Cell Imaging of MCF10A Cells Treated with EGF or PBS
<p>MCF10A cell culture and experimental procedures were conducted based on established methodologies (10.1038/s42003-022-03975-9). For routine maintenance and passaging, cells were cultured in a growth medium composed of DMEM/F12 (Invitrogen, #11330-032) supplemented with 5% horse serum (Sigma, #H1138), 20 ng/ml EGF (R&D Systems, #236-EG), 0.5 µg/ml hydrocortisone (Sigma, #H-4001), 100 ng/ml cholera toxin (Sigma, #C8052), 10 µg/ml insulin (Sigma, #I9278), and 1% Penicillin/Streptomycin (Invitrogen, #15070-063). For experiments involving EGF perturbation, a growth factor-free medium was prepared using DMEM/F12, 5% horse serum, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and 1% Pen/Strep.</p> <p>Cells were cultured to 50–80% confluency before being detached with 0.05% trypsin-EDTA (Thermo Fisher Scientific, #25300-054). Subsequently, 20,000 cells were seeded into 24-well plates (Thermo Fisher Scientific, #267062) coated with collagen-1 (Cultrex, #3442-050-01) in growth medium. After six hours, the cells were rinsed with PBS, and the medium was replaced with growth factor-free medium. Following an 18-hour period of growth factor deprivation, cells were treated with either PBS or 10 ng/ml EGF (R&D Systems, #236-EG).</p> <p>Phenotypic responses to EGF treatment were assessed through live-cell imaging using the Incucyte S3 microscope (Essen BioScience, #4647), which captured images every 30 minutes over a 24-hour period. The dataset includes an Excel spreadsheet that documents the experimental conditions for each imaged well.</p>
Raw data accompanying the manuscript "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse"
<p>These are the raw datasets used to generate the figures for the manuscript entitled "Cost-effective high-speed, three-dimensional live-cell imaging of HIV-1 transfer at the T cell virological synapse". The data files are 3D image stacks of a custom-built wide field deconvolution fluorescence microscope (.tif) and super-resolution structured illumination microscopy data (.dv) of Jurkat T cells transferring HIV-1 virus particles to previously uninfected primary T cells.</p>
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
<p>3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data</p> <p>From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03.003178</p>
Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction
<p>The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.</p>
Live-Cell Imaging of MCF10A Cells Treated individually or in combination with EGF, OSM, or TGFB
<p>MCF10A cell culture and experimental procedures were conducted based on established methodologies (10.1038/s42003-022-03975-9). For routine maintenance and passaging, cells were cultured in a growth medium composed of DMEM/F12 (Invitrogen, #11330-032) supplemented with 5% horse serum (Sigma, #H1138), 20 ng/ml EGF (R&D Systems, #236-EG), 0.5 µg/ml hydrocortisone (Sigma, #H-4001), 100 ng/ml cholera toxin (Sigma, #C8052), 10 µg/ml insulin (Sigma, #I9278), and 1% Penicillin/Streptomycin (Invitrogen, #15070-063). For experiments involving EGF perturbation, a growth factor-free medium was prepared using DMEM/F12, 5% horse serum, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and 1% Pen/Strep.</p> <p>Cells were cultured to 50–80% confluency before being detached with 0.05% trypsin-EDTA (Thermo Fisher Scientific, #25300-054). Subsequently, 20,000 cells were seeded into 24-well plates (Thermo Fisher Scientific, #267062) coated with collagen-1 (Cultrex, #3442-050-01) in growth medium.<span>After an 18-hour incubation in the new media, cells were treated with </span><span>single </span><span>ligand</span><span> or </span><span>combinations of ligands</span><span> in fresh growth factor-free media: 10 ng/ml EGF (R&D Systems #236-EG), 10 ng/ml OSM (R&D Systems #8475-OM), and 10 ng/ml TGFβ (R&D Systems #240-B).</span></p> <p>Phenotypic responses to individual and combination treatment with EGF, OSM, and TGFB treatment were assessed through live-cell imaging using the Incucyte S3 microscope (Essen BioScience, #4647), which captured images every 30 minutes over a 24-hour period. The dataset includes an Excel spreadsheet that documents the experimental conditions for each imaged well.</p> <p>Companion RNAseq <span><span>can be accessed from the Gene Expression Omnibus</span><span>: </span><span>GSE282654</span><span>.</span></span><span> </span></p>
Live-cell imaging of LLC-PK1 cells microtubule dynamics
<p>Stable LLC-PK1 cell line (ATCC:CL-101) was generated and provided by Michael W. Davidson [1,2]. Using a Zeiss Celldiscoverer 7 microscope with a 100X/1.47 NA oil-immersion objective (Plan-Apochromat, Zeiss) and a sCMOS sensor (Hamamatsu, ORCA-Fusion, C15440-20UP), cultured LLC-PK1 cells expressing mEmerald-EB3 were imaged with a 43 nm pixel size. Exposure time was 100 ms, with each frame being captured every two seconds. During acquisition, temperature and CO2 control was set to 37°C and 5%, respectively. mEmerald-EB3 was excited using a 488 nm laser at 1% power, with a FITC filter for fluorescence collection. Acquisition software ZEN 3.2 (blue edition) was used for the imaging protocol.</p> <p>1. Rizzo, M. A., Davidson, M. W., & Piston, D. W. (2009). Fluorescent protein tracking and detection: fluorescent protein structure and color variants. Cold Spring Harbor Protocols, 2009(12), pdb-top63.</p> <p>2. Huang, F., Hartwich, T., Rivera-Molina, F. et al. Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms. Nat Methods 10, 653–658 (2013).</p>
"CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data" datasets
<p>Datasets from the article:</p> <p><strong>CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data </strong></p> <p>by Franck Simon, Maria Colomba Comes, Tiziana Tocci, Louise Dupuis, Vincent Cabeli, Nikita Lagrange, Arianna Mencattini, Maria Carla Parrini, Eugenio Martinelli, Hervé Isambert.</p> <p> </p> <p>The <strong>original videos</strong> are uploaded as: "20161230.zip", "20170105.rar", "Video_2017_0517.zip".</p> <p><strong>Details </strong>for each <strong>experiment </strong>can be found in: "Experiments' details.zip".</p> <p>The <strong>ROIs </strong>(ROI: Region of Interest) are uploaded as .tif files in: "EXTRACTED ROIs.zip".</p> <p>The <strong>MATLAB data</strong> is uploaded in "MATLAB_DATA.rar" and includes: the cancer cells' trajectories (subfolder: "TUMOR TRAJECTORIES"), the immune cells' trajectories (subfolder: "IMMUNE TRAJECTORIES"), the ROIs videos as .mat files for the detection of cells (subfolder: "ROI MAT"), the ROIs further cropped for the extraction of shape descriptors (folder: "ROI_TU MAT"). The ROIs videos .mat files included in the last two subfolders are stopped after their apoptosis has been detected.</p>
Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms
Open the record for dataset details and reuse information.
Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction
Open the record for dataset details and reuse information.
Live-cell imaging data set of HaCaT FUCCI cells with BF/DIC and fluorescence
<p>This dataset contains time-lapse acquisitions of HaCaT FUCCI cells cultured in 8-well chambered coverslips with fluorobrite media. Cells were provided by Dr. Francesco Pasqualini and Dr. Moises di Sante (<a title="http://www.syntheticphysiologylab.com/" href="http://www.syntheticphysiologylab.com/" target="_blank" rel="noreferrer noopener">http://www.syntheticphysiologylab.com</a>), and videos acquired at the Henriques Lab (<a title="https://henriqueslab.org/" href="https://henriqueslab.org/" target="_blank" rel="noreferrer noopener">https://henriqueslab.org/</a>). </p> <p>HaCaT_FUCCI_BF-live set: Nikon Ti2, Channels BF (16 bit), FITC (12 bit sensitive) and Cy5 (12 bit sensitive). 20 positions, acquired in Nikon Ti2 with a 20x/0.8, every 30 minutes for 18 hours. </p> <p><span>HaCaT_FUCCI_DIC-live set: Nikon Ti2, Channels DIC, FITC and Cy5 (all 12 bit sensitive). 20 positions, acquired in Nikon Ti2 with a 20x/0.8, every 30 minutes for 18 hours. </span></p>
Conformational changes in insulin receptor illuminated by live-cell linear dichroism imaging and a FLIP biosensor
<p>Response of GP2(1)-eGFP-CD59, a FLIP biosensor co transfected with insulin receptor against anatgonists and agonists of IR was measured and qunatified using polarization-resolved fluorescence microscopy. Linear dichoirism values were measured by analyinzing cells using already published imageJ macros (Bondar, Rybakova et al. 2021). This data set contains both raw images obtained from polarization micrscopy and analyzed data.</p>
Quantitative live-cell imaging of secretion activity reveals dynamic immune responses
GEO Series GSE253100. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
A live-cell image-based machine learning strategy for reducing variability in iPSC differentiation systems
GEO Series GSE226159. Homo sapiens. 45 samples. Type: Expression profiling by high throughput sequencing.
Decoding the interplay between m6A modification and stress granule stability by live-cell imaging
GEO Series GSE273366. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Combined multiphoton live-cell imaging and molecular systems approaches reveal mosaic contribution of dynamic transiently signaling INPs to the adult Dentate Gyrus NSC niche
GEO Series GSE50148. Mus musculus. 11 samples. Type: Expression profiling by array.
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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.