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61 results for “light sheet”
(08)-Strobl2021A-DS0001 – Tribolium castaneum AGOC{Zen1'#O(LA)-mEmerald} #1 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(08)-Strobl2021A-DS0001 – <em>Tribolium castaneum</em> AGOC{Zen1'#O(LA)-mEmerald} #1 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(07)-Ratke2020A-DS0005 – Tribolium castaneum AGOC{Zen1'#O(LA)-mEmerald} #2 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0005 – <em>Tribolium castaneum</em> AGOC{Zen1'#O(LA)-mEmerald} #2 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(07)-Ratke2020A-DS0004 – Tribolium castaneum AGOC{Zen1'#O(LA)-mEmerald} #1 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(07)-Ratke2020A-DS0004 – <em>Tribolium castaneum</em> AGOC{Zen1'#O(LA)-mEmerald} #1 subline long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(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>
U-Net model trained on Ascadian embryo dataset of light sheet microscope
<p>U-Net model trained using CARE package for doing semantic segmentation of Ascadian embryo</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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Data for: Characterization, comparison, and optimization of lattice light sheets (Part 3/3)
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Data for: Characterization, comparison, and optimization of lattice light sheets (Part 2/3)
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Data for: Characterization, comparison, and optimization of lattice light sheets (Part 1/3)
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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>
Zeiss Lattice Light Sheet 7 Point Spread Functions and example dataset
<p>This repository contains some point spread functions (PSFs) distilled from imaging fluorescent beads, 200nm, <a href="https://www.thermofisher.com/order/catalog/product/F8811?SID=srch-srp-F8811" target="_blank" rel="noopener noreferrer">F8811</a> in an agarose gel, on a Zeiss Lattice Light sheet 7 microscope. The bead images from which the PSF were distilled are contained in this repo.</p> <p>Several images were acquired with varying settings of the light sheet (light sheet was always set as the 30 um x1000 nm).</p> <p>These three parameters were varied:</p> <p>FS: focus sheet (-100, -75, -25, 0)</p> <p>FW: focus waist (40, 45, 50, 55, 60, 65, 70, 75, 80, 85)</p> <p>AC: aberration control (150, 155, 160, 165, 170, 175, 180, 185, 190)</p> <p>The file psf-200nm correspond to the best settings taken between the different settings. The two other files (psf-300nm, psf-400nm) correspond to resampled versions of the psf-200nm file.</p> <p>The all-psfs.tif contains the deskewed psf ordered similarly as the poster uploaded in this version of the repository (ELMI-2024-poster.pdf).</p> <p>A sample czi file (Hela Kyoto, raw data) is provided to test deconvolution algorithms.</p> <p>Note that none of these data is deskewed.</p> <p>--------------------</p> <p>Here's a protocol to prepare a gel containing beads at a good enough density:</p> <ul> <li> <p>Material:</p> <ul> <li>Agarose 2%</li> <li>Fluorescent beads, 200nm, <a href="https://www.thermofisher.com/order/catalog/product/F8811?SID=srch-srp-F8811">F8811</a>. Stock is 1000x</li> </ul> </li> <li> <p>Protocol:</p> <ul> <li>Put the agarose to warm up at 90C.</li> <li>Vortex the beads stock.</li> <li>Dilute a 100 times the bead dilution in PBS (10 uL in 1mL), vortex.</li> <li>Prepare a clean slide, and a clean coverglass (22x22mm).</li> <li>Take 90uL of agarose, put in a 1.5mL tube, add 10uL of the diluted beads, vortex.</li> <li>Take 50uL of this agarose solution, put it on the slide, add the coverglass on top.</li> <li>Put this slide in the fridge and wait a few minutes.</li> <li>Use nailpolish to seal the coverglass. Wait long enoughfor the nailpolish to dry.</li> </ul> </li> </ul> <p>You should a gel of about 100um thickness.</p> <p>It should be possible to add a bit of free dye in the gel in order to help focusing the light sheet. Ideally a bit of far-red free dye, like Alexa 647.</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.