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324
datasets available to search
ShareScore release 0.9.0
Dataset results
324 results for “fluorescent imaging”
Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation.
<p>This data set contains a set of fluorescent microscopy images of a co-culture of neutrophil cells and E. coli bacteria used to study the Neutrophil Extracellular Trap (NET) formation stimulated by bacteria. </p> <p>NETs and live cells were visualized with a double fluorescent staining of DNA using Hoechst 33342 and SYTOX Green. </p> <p><strong>Reagents.</strong></p> <p>Roswell Park Memorial Institute (RPMI) 1640 medium, HEPES, SYTOX<sup>TM</sup> Green, and Hoechst 33342 were purchased from Thermo Fisher Scientific (Waltham, USA). LB broth was purchased from Sigma Aldrich (St Louis, MO, USA).</p> <p><strong>Preparation of blood neutrophils.</strong></p> <p>Neutrophils were obtained from peripheral blood of one healthy blood donor. Blood sample was purchased at Local Blood Donation Centre and according to local regulations, the blood donor enabled blood donation center to sell their blood samples for scientific purposes and the consent of bioethical committee was not required. Blood was collected into a citrate tube and processed within 2 hours from collection. Neutrophils were isolated using density gradient centrifugation followed by polyvinyl alcohol sedimentation, exactly as described in [1]. Isolated neutrophils were suspended in RPMI 1640 medium with 10 mM HEPES (RH). </p> <p><strong>Preparation of bacteria.</strong></p> <p><em>Escherichia coli</em> (American Type Culture Collection(ATCC) 25922 strain) were grown overnight in LB broth with shaking. In the morning, an aliquot of bacterial culture was taken, diluted 100 x in a fresh LB medium and grown for subsequent 2-3 hours. Subsequently, bacterial cultures were washed and resuspended in RH medium.</p> <p><strong>Co-culture of neutrophils with bacteria</strong><br> Neutrophils were seeded into the wells of 48-well plates at the density of 2 ⨉ 10<sup>4</sup> cells/well and allowed to settle for 30 minutes at 37°C, 5% CO2. Subsequently, <em>E. coli</em> was added into the appropriate wells at the multiplicity of infection of 4 or 1 (<em>E.coli</em>: neutrophil). Neutrophils incubated without bacteria were used as a control group. A technical duplicate for each condition was prepared. <br> For each intended timepoint (t=0, 60, 90, 120, 180 minutes), a separate 48 well plate was prepared. The plates were centrifuged for 5 minutes at 250 g to allow the contact of bacteria with neutrophils. The plates were incubated at 37°C, 5\% CO2 for a specified time and then the samples were stained with SYTOX<sup>TM</sup> Green (100 nM) and Hoechst 33342 (1.25 μM) for 10 minutes. Four images of each well were taken with Leica DMi8 fluorescent microscope equipped with a 10× magnification objective (Leica, Wetzlar, Germany). Overall, 120 images have been obtained.</p> <p> </p> <p><strong>2019_04_24--ecoli_neu_tiff_channel_merged.zip:</strong> Images in .tif format, each containing 5 channels: channel 1 for SYTOX Green fluorescent stain (green fluorescence), channel 2 for Hoechst 33342 fluorescent stain (blue fluorescence), and three channels for transmission light encoded in RGB values. </p> <p> </p> <p><strong>2019_04_24--ecoli_neu_tiff_raw_exported.zip:</strong> Images split by different light sources: transmission light (_ch00.tif), SYTOX Green fluorescence (_ch01.tif), Hoechst 33342 fluorescence (_ch02.tif).</p> <p> </p> <p>[1] Bystrzycka W, Moskalik A, Sieczkowska S, Manda-Handzlik A, Demkow U, Ciepiela O. The effect of clindamycin and amoxicillin on neutrophil extracellular trap (NET) release. <em>Cent Eur J Immunol</em>. 2016;41(1):1-5. doi:10.5114/ceji.2016.58811</p>
Two-photon fluorescence microscopy image stacks of human brain sections (grey and white matter)
<p>Two-photon fluorescence microscopy (TPFM) image stacks of human brain sections including grey matter (N<sub>g</sub>=10) and white matter (N<sub>w</sub>=10), considered in the validation of the 3D fiber orientation analysis pipeline proposed in: "<em>Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy</em>". <br> Human brain tissue was preliminarily treated for TPFM following the label-free MAGIC preparation technique, presented in (Costantini et al., <em>Scientific Reports</em> 2021).</p> <p>The PSF of the TPFM system has a FWHM of (0.692, 0.692, 2.612) μm along the x, y, and z axes, respectively, whereas the adopted voxel size is 0.88 μm x 0.88 μm x 1 μm.</p>
Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript
<p>Supplementary videos for preprint manuscript: </p> <p><em>Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture</em><br> Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby<br> bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043</p> <p>All videos have been rendered with JPEG compression.</p> <p>Shortened video captions (Please see supplementary information document for full caption)<br> <strong>Video 1:</strong> 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients. <br> <strong>Video 2:</strong> Widefield transillumination timelapse of hiPSC-CM and adult-CM <br> <strong>Video 3:</strong> Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients. <br> <strong>Video 4a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 4b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 5a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 5b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 6a</strong>: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb. <br> <strong>Video 6b:</strong> Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 7a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 7b: </strong>Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb. </p> <p> </p>
Example of Fluorescence Lifetime Imaging Microscopy (FLIM) image stack in .ptu format
<p>The dataset is a 3D stack of fluorescence lifetime imaging microscopy (FLIM) images in ptu format to be used as test and training data. It contains the original .lif file (1) with the stack and a single plane image (to be opened using LAS X and LAS X SMD FLIM), exported raw FLIM data in .ptu format of the stack (3) and the single plane (2a) (to be opened in software capable of reading .ptu files) as well as an intensity image in .tif format (2b) of the single plane for a quick sample overview.</p> <p>The sample is a cross-section of hazel (<em>Corylus avellana</em>) 'diclinous male flower t.s.' with Etzold staining provided by the company Zeiss (CZ 01/05). The dataset was generated using a Leica Stellaris 8 upright confocal laser scanning microscope using a 93x/1.4 glycerol immersion objective. Each image of the 65 slice stack with z step size of 0.287 µm contains 512 x 512 pixels with a pixel size of 0.078 µm x 0.078 µm. Excitation was done with a white-light laser at 491 nm and a laser pulse rate of 40 MHz and a pixel dwell time of 2.0875 µs. Images were acquired using a HyD X detector in counting mode in the spectral range of 496 to 739 nm using Leica Application Suite X (LAS X) version 4.4.0.24861 and LAS X SMD FLIM version 4.5.0 for FLIM image acquisition. 10 frames were accumulated per image. Metadata is available as text file (4a) and as metadata files from LAS X (4b).</p>
FIOLA: an accelerated pipeline for Fluorescence Imaging OnLine Analysis calcium dataset
<p>The dataset was used in paper FIOLA: an accelerated pipeline for Fluorescence Imaging OnLine Analysis named as 1MP. The dataset was only used to test FIOLA motion correction performance.<br> The dataset was collected for the paper Sensory-driven enhancement of calcium signals in individual Purkinje cell dendrites of awake mice (link: https://pubmed.ncbi.nlm.nih.gov/24582958/) but never published before. Data was recorded in the left lobule of the cerebellum of an awake mouse using the calcium indicator GCaMP6f. GCaMP6f was selectively expressed in Purkinje cells via a combinatorial virus strategy (as explained in the paper).</p> <p>For other datasets used in paper FIOLA, check the original paper and sources they were published.</p> <p> </p> <p> </p>
UniFMIR: Pre-training a Foundation Model for Universal Fluorescence Microscopy Image Restoration
<p>This repository contains the preprocessed dataset for [UniFMIR](https://github.com/cxm12/UNiFMIR/). All training and test data involved in the experiments are publicly available datasets. Licenses of the original dataset are applied. You can refer to the Github repository for details.</p> <p>* The 3D denoising/isotropic reconstruction/projection datasets can be downloaded from [Content Aware Image Restoration dataset](https://publications.mpi-cbg.de/publications-sites/7207/). `Projection_Flywing/train_data/my_training_data.npz` are generated according to the [CSBDeep](http://csbdeep.bioimagecomputing.com/doc/).</p> <p>* The SR dataset can be downloaded from [BioSR dataset](https://doi.org/10.6084/m9.figshare.13264793). The dataset is augmented according to the instructions in [DFCAN](https://github.com/qc17-THU/DL-SR/tree/main#train-a-new-model) and `my_training_data.npz` files are generated following [CSBDeep](http://csbdeep.bioimagecomputing.com/doc/datagen.html). </p> <p>* The Volumetric reconstruction dataset are from [VCD-LFM dataset](https://doi.org/10.5281/zenodo.4390067). The dataset is prepared according to the instructions in [VCD-Net](https://github.com/feilab-hust/VCD-Net).</p> <p>* DeepBacs dataset can be downloaded from [DeepBacs dataset](https://zenodo.org/record/6460867). We split the dataset into 5 folds for cross-validation. Shareloc dataset can be downloaded from [Shareloc dataset](https://zenodo.org/record/7234161).</p> <p> </p> <p>The data paths should be as follows:</p> <p>```</p> <p>VCD/vcdnet/</p> <p>CSB/DataSet/</p> <p> Denoising_Planaria/</p> <p> Denoising_Tribolium/</p> <p> Isotropic/Isotropic_Liver/</p> <p> Projection_Flywing/</p> <p> BioSR_WF_to_SIM/DL-SR-main/dataset/</p> <p> Synthetic_tubulin_gfp/</p> <p> Synthetic_tubulin_granules/</p> <p>DeepBacs/</p> <p>Shareloc/</p> <p>```</p>
Code and data for: Decoupling channel count from field-of-view and spatial resolution in single-sensor imaging systems for fluorescence image-guided surgery
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Raw fluorescent images of the stem cell based embryoids
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Synergistic label-free fluorescence imaging and miRNA studies reveal dynamic human neuron-glial metabolic interactions following injury
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Fluorescence images of ybx1 mutant neuromasts [time course, wt]
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Fluorescence images of ybx1 mutant neuromasts [time course, het]
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Fluorescence time-lapse images of MDA-MB-231 cells expressing FUCCI(CA)2 (Part 1/2)
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Fluorescence images of ybx1 mutant neuromasts [incross]
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Fluorescence images of ybx1 mutant neuromasts [Ybx1 immunofluorescence]
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Fluorescent microscopy images of larval zebrafish of either TraNac, Nacre or WT background
<p><strong>The images show larval zebrafish at 5 days post-fertilization using fluorescent microscopy. The fish are either of Nacre, TraNac, or WT background. The fluorescent channels are either GFP, YFP or mCherry. </strong></p>
Fluorescent (C)LSM image sequences of Dictyostelium discoideum (Ax2 - LifeAct mRFP) for cell track and cell contour analysis
<p>This data set is designed for cell contour and cell track analysis. Hence image sequences of moving Dictyostelium discoideum cells are recorded. For the purpose to facilitate the detection of the cell contour we take fluorescent images of the cortical protein actin to obtain a high contrast between background and cell body. In each image sequences several cells are recorded. This allows for an analysis of all cells at once or to crop single cell tracks.</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>
Dataset related to article "Evaluation of cell metabolic adaptation in wound and tumour by fluorescence Lifetime imaging Microscopy"
<p>This record contains data related to article "Evaluation of cell metabolic adaptation in wound and tumour by fluorescence Lifetime imaging Microscopy"</p> <p>Abstract</p> <p>Acidic pH occurs in acute wounds progressing to healing as consequence of a cell metabolic adaptation in response to injury-induced tissue hypoperfusion. In tumours, high metabolic rate leads to acidosis affecting cancer progression. Acidic pH affects activities of remodelling cells in vitro. The pH measurement predicts healing in pathological wounds and success of surgical treatment of burns and chronic ulcers. However, current methods are limited to skin surface or based on detection of fluorescence intensity of specific sensitive probes that suffer of microenvironment factors. Herein, we ascertained relevance in vivo of cell metabolic adaptation in skin repair by interfering with anaerobic glycolysis. Moreover, a custom-designed skin imaging chamber, 2-Photon microscopy (2PM), fluorescence lifetime imaging (FLIM) and data mapping analyses were used to correlate maps of glycolytic activity in vivo as measurement of NADH intrinsic lifetime with areas of hypoxia and acidification in models of skin injury and cancer. The method was challenged by measuring the NADH profile by interfering with anaerobic glycolysis and oxidative phosphorylation in the mitochondrial respiratory chain. Therefore, intravital NADH FLIM represents a tool for investigating cell metabolic adaptation occurring in wounds, as well as the relationship between cell metabolism and cancer.</p>
Data from: Bio-inspired imager improves sensitivity in near-infrared fluorescence image-guided surgery
Image-guided surgery can enhance cancer treatment by decreasing, and ideally eliminating, positive tumor margins and iatrogenic damage to healthy tissue. Current state-of-the-art near-infrared fluorescence imaging systems are bulky and costly, lack sensitivity under surgical illumination, and lack co-registration accuracy between multimodal images. As a result, an overwhelming majority of physicians still rely on their unaided eyes and palpation as the primary sensing modalities for distinguishing cancerous from healthy tissue. Here we introduce an innovative design, comprising an artificial multispectral sensor inspired by the Morpho butterfly's compound eye, which can significantly improve image-guided surgery. By monolithically integrating spectral tapetal filters with photodetectors, we have realized a single-chip multispectral imager with 1000× higher sensitivity and 7× better spatial co-registration accuracy compared to clinical imaging systems in current use. Preclinical and clinical data demonstrate that this technology seamlessly integrates into the surgical workflow while providing surgeons with real-time information on the location of cancerous tissue and sentinel lymph nodes. Due to its low manufacturing cost, our bio-inspired sensor will provide resource-limited hospitals with much-needed technology to enable more accurate value-based health care.
Data from: Combined fluorescent and electron microscopic imaging unveils the specific properties of two classes of meiotic crossovers
<p>Crossovers (COs) shuffle genetic information and allow balanced segregation of homologous chromosomes during the first division of meiosis. Recombination nodules (RNs) are closely correlated with crossing over, and, because they are observed by electron microscopy of synaptonemal complexes (SCs) in extended pachytene chromosomes, RNs provide the highest-resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes. In several organisms, mutants demonstrate that two molecularly distinct pathways produce COs. One pathway produces class I COs that exhibit interference (lowered probability of nearby COs), and the other pathway produces class II COs with little or no interference. However, the relative contributions, genomic distributions, and interactions of these two pathways are essentially unknown in nonmutant organisms because marker segregation only indicates that a CO has occurred, not its class type. Here, we combine the efficiency of light microscopy for revealing cellular functions using a fluorescent probe to MLH1 proteins to mark class I COs with the high resolution of electron microscopy to localize and characterize all COs (RNs) in the same sample of meiotic pachytene chromosomes from wild-type tomato. To our knowledge, for the first time, every CO along each chromosome can be identified by class to unveil specific characteristics of each pathway. We find that class I (MLH1-positive) and class II (MLH1-negative) COs have different recombination profiles along chromosomes. In particular, class II COs, which represent about 18% of all COs, exhibit no interference and are disproportionately represented in pericentric heterochromatin, a feature potentially exploitable in plant breeding. Finally, our results demonstrate that the two pathways are not independent because there is interference between class I and II COs.</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.