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Dataset results
43 results for “Light sheet microscopy”
(07)-Ratke2020A-DS0003 – Drosophila melanogaster w[*]; P{w[+mC]=His2Av-EGFP.C}2/SM6a line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0003 – <em>Drosophila melanogaster</em> w[*]; P{w[+mC]=His2Av-EGFP.C}2/SM6a line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(07)-Ratke2020A-DS0001 – Drosophila melanogaster y[1] w[67c23]; P{w[+mC]=Ubi-GFP.nls}ID-2; P{Ubi-GFP.nls}ID-3 line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0001 – <em>Drosophila melanogaster</em> y[1] w[67c23]; P{w[+mC]=Ubi-GFP.nls}ID-2; P{Ubi-GFP.nls}ID-3 line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(07)-Ratke2020A-DS0002 – Drosophila melanogaster w[*]; P{w[+mC]=Tub84B-EGFP.NLS}3 long-term live imaging dataset acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0002 <em>–</em> <em>Drosophila melanogaste</em>r y[1] w[67c23]; P{w[+mC]=Ubi-GFP.nls}ID-2; P{Ubi-GFP.nls}ID-3 (Bloomington <em>Drosophila</em> Stock Center #29724) long-term live imaging dataset acquired with light sheet fluorescence microscopy</p>
(08)-Strobl2021A-DS0003 – Tribolium castaneum Gruul #1 hybrid line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(08)-Strobl2021A-DS0003 – <em>Tribolium castaneum</em> Gruul #1 hybrid line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(07)-Ratke2020A-DS0006 – Tribolium castaneum AGOC{Zen1'#O(LA)-mEmerald} #3 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0006 – <em>Tribolium castaneum</em> AGOC{Zen1'#O(LA)-mEmerald} #3 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
Dataset for Adaptive Light-Sheet Fluorescence Microscopy with a Deformable Mirror for Video-Rate Volumetric Imaging
<p>1. Underlying data of figures in the paper </p> <p>2. Background images used to process the experimental data</p> <p>3. image stack of 250 nm beads</p> <p>4. image stack of sunflower pollen grains</p> <p>5. image stacks and videos of Fluo-4 labelled cells</p> <p>6. image stacks and videos of CMO-labelled cells</p> <p>The data is organised according to the figures they are related to in the following publication:</p> <p> </p> <p><a href="https://aip.scitation.org/author/Hong%2C+Wenzhi">Wenzhi Hong</a><em>, </em><a href="https://aip.scitation.org/author/Wright%2C+Terry">Terry Wright</a><em>, </em><a href="https://aip.scitation.org/author/Sparks%2C+Hugh">Hugh Sparks</a><em>, </em><a href="https://aip.scitation.org/author/Dvinskikh%2C+Liuba">Liuba Dvinskikh</a><em>, </em><a href="https://aip.scitation.org/author/MacLeod%2C+Ken">Ken MacLeod</a><em>, </em><a href="https://aip.scitation.org/author/Paterson%2C+Carl">Carl Paterson</a><em>, and </em><a href="https://aip.scitation.org/author/Dunsby%2C+Chris">Chris Dunsby</a> </p> <p>, "Adaptive light-sheet fluorescence microscopy with a deformable mirror for video-rate volumetric imaging", Appl. Phys. Lett. 121, 193703 (2022) <a href="https://doi.org/10.1063/5.0125946">https://doi.org/10.1063/5.0125946</a></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>
Data for: Image processing tools for petabyte-scale light sheet microscopy data (Part 2/2)
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Data for: Image processing tools for petabyte-scale light sheet microscopy data (Part 1/2)
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Data from: Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology
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I2K2020 Data for "Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data"
<p>Example data for the I2K2020 tutorial "Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data" (https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends/virtual-workshop-program)</p> <p>"Readme" file for data description included in folder.</p> <p><strong>Background:</strong> Zebrafish transgenic lines and light sheet fluorescence microscopy (LSFM) allow unrivalled insights into vascular development <em>in vivo</em> and 3D. The vascular architecture can be used to describe physiological status. However, assessment of the vasculature still relies on individual visual assessment rather than objective quantification. Thus, an image analysis pipeline is required to allow data assessment in 3D robustly and sensitively, while being able to handle LSFM data.</p> <p>Kugler et al have produced an image analysis workflow to quantify the zebrafish brain vasculature in 3D (https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2).</p> <p><strong>Aim</strong>: In this tutorial we will use the analysis workflow produced by Kugler et al to examine and quantify the zebrafish brain vasculature in 3D with a hands-on practical (https://github.com/ElisabethKugler/ZFVascularQuantification).</p>
(12)-Pereyra2024A-DS0001--0009 – Nine Tribolium castaneum long-term live imaging datasets of embryonic development acquired with light sheet fluorescence microscopy
<p>(12)-Pereyra2024A-DS0001--0009 – Nine <em>Tribolium castaneum</em> long-term live imaging datasets of embryonic development acquired with light sheet fluorescence microscopy</p>
Octopus vulgaris, Sepia officinalis, Loligo vulgaris and Illex coindetii early life phases Light Sheet Fluerescence Microscopy (LSFM) 3D scans.
<p>Acronyms: OV: <em>Octopus vulgaris</em>, SO: <em>Sepia officinalis</em>, LV: <em>Loligo vulgaris</em>, IC: <em>Illex coindetii</em>, DPH: Days Post-Hatching.</p> <p>Two detection objectives were used, depending on sample size, a 4x/0.28 NA Olympus XLFLUOR4x/340 objective (0, 5, 10, 19 DPH <em>Octopus vulgaris</em> individuals,<em> Loligo vulgaris</em> and<em> Illex coindetii</em>) and a Nikon 10x/0.5 NA CFI Plan Apochromat 10xC Glyc (Rest of the samples). For illumination, two 4x/0.95 NA Nikon CFI Plan Apo Lambda 4x were used when using the 10x detection objective and two 4x/0.13 NA Nikon Plan Fluor illumination objectives were used when using the 4x detection objective. </p> <p>Microscope: MuVi SPIM (Luxendo), LCS SPIM (Luxendo, only <em>Sepia officinalis</em> and 60 DPH <em>Octopus vulgaris</em> individuals).</p> <p>All the data has been scaled in order to reduce file sizes. Full size stacks can be requested to dgvilar@gmail.com.</p>
(06)-He2019A-DS0001 – Tribolium castaneum foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(06)-He2019A-DS0001 – <em>Tribolium castaneum</em> foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
Microvascular network remodeling in the ischemic brain defined by light sheet microscopy
<p>This dataset contains the raw image data set used in the study entitled "Microvascular network remodeling in the ischemic brain defined by light sheet microscopy" by Hagemann et al.. Images were analysed using VesselExpress software (see also <a href="https://pubmed.ncbi.nlm.nih.gov/37056368/">https://pubmed.ncbi.nlm.nih.gov/37056368/</a>) using the provided config file with gamma values ranging from 50 to 400.</p>
Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy
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Code and dataset for: Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy
<p>Dataset and codes for: Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy.</p> <p>Published online via First Release, <strong>11 June 2020</strong></p> <p>B. Qin et al., Science, 10.1126/science.abb8501 (2020).</p> <p> </p>
Representative data accompanying the manuscript: Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases
<p>Representative data accompanying the manuscript: Sinclair R, Wang M, Jawaid MZ, Longkumer T, Aaron J, Rossetti B, Wait E, McDonald K, Cox D, Heddleston J, Wilkop T, Drakakaki G. (2024). <em>Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases.</em> J Exp Bot. 2024 Mar 4: erae091. doi: 10.1093/jxb/erae091.</p> <p>The data show YFP–RABA2a dynamics in dividing cells of Arabidopsis root tips using lattice light sheet microscopy. Treatments with or without Endosidin 7, a cytokinesis-specific callose deposition inhibitor, are shown.</p> <p>Data: </p> <p>22.3 YFP-RABA2A. </p> <p>23.9 YFP-RABA2A ES7 </p>
3D Reconstruction of Neuronal Allometry and Neuromuscular Projections in Asexual Planarians Using Expansion Tiling Light Sheet Microscopy dataset2
<p>wide type planarian 6G10 staining taken with TLSM</p>
(11)-Strobl2023A-DS0001--0010 – Ten Tribolium castaneum long-term live imaging datasets of embryonic development acquired with light sheet fluorescence microscopy
<p>(11)-Strobl2023A-DS0001--0010 – Ten <em>Tribolium castaneum</em> long-term live imaging datasets of embryonic development acquired with light sheet fluorescence microscopy</p>
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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.