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Dataset results
61 results for “light sheet”
3D dataset of root soil bacteria dynamics obtained using large field of view light sheet microscope
<p>A tailor made dual-illumination light-sheet system acquired photons scattered from the plant whilst fluorescence emissions were simultaneously captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm<sup>3</sup> in size with as good as 5 µm resolution at a rate of up to one scan every 30 minutes. The dataset shows the dynamics of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time.</p> <p> </p> <p> </p>
VesselExpress: Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs
<p>This dataset contains raw, segmented and skeletonized 3D light-sheet microscopic image volumes of blood vessels of different organs which were processed by VesselExpress. Please find the software here: https://github.com/RUB-Bioinf/VesselExpress. For details on how to run and setup the software please watch our tutorial (https://youtu.be/a8GWVKJNh68).</p>
Multiscale light-sheet organoid imaging framework
<p>These two files correspond to the data associated with the light-sheet recordings and time-course recordings utilized for the manuscript entitled "Multiscale light-sheet organoid imaging framework".<br> If access to the imaging data is needed, (which in total comprises of ~700 GB), please contact Prisca Liberali (prisca.liberali@fmi.ch) for more information.</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>
Fused image dataset from light sheet microscope
<p>Example dataset that ships with VollSeg Napari samples, providing a 3D imaged dataset of fused Acadian embryo imaged with light sheet and fused over 4 angles.</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>
4D light sheet imaging, computational reconstruction, and cell tracking in mouse embryos -- example data (raw .czi and fused .klb light sheet images of mouse E7.5)
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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>
Lattice light sheet data
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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>
Light sheet acquisitions
<p>Example datasets used to validate remote focus light sheet model. One dataset is an example light sheet imaged in transmission. The other is a 200um zstack of beads illuminated with a static light sheet. The analysis code can be found in our Github repository, DOI 10.5281/zenodo.12752312.</p>
3D Interferometric Lattice Light-Sheet Imaging
<p>This repository contains experimental data and code supporting the publication: Cao <em>et al.</em>, Volumetric Interferometric Lattice Light Sheet Imaging.<strong><em>Nat. Biotechnol. </em></strong>(2021), DOI: https://doi.org/10.1038/s41587-021-01042-y</p> <p>Details about the files are provided in the Readme files in the associated sub-folders.</p> <p>3D-iLLS setup photos can be found in https://github.com/PertsinidisLab/3D-iLLS-photos</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>
Second wave, late-phase neuroinflammation in the brain of aged 5xFAD transgenic Alzheimer's disease model mice iden-tified using macrolaser light sheet microscopy imaging with tissue clearing
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Light-sheet microscopy enabled by a miniaturized plane illuminator
<p>Light-sheet microscopy enabled by a miniaturized plane illuminator </p>
Demo Datasets for Non-light-sheet Imaging Modalities for PetaKit5D
<p>Demo dataset for PetaKit5D (<a href="https://github.com/abcucberkeley/LLSM5DTools">https://github.com/abcucberkeley/PetaKit5D</a>). </p> <p>There are four datasets for non-light-sheet modalities: 2-photon, confocal, oblique illumination "phase", and widefield. Some demos in PetaKit5D use this dataset to demonstrate the usage. Please refer to the readme.txt for the file structures, parameters, and other information.</p> <p>Please cite our paper (<a href="https://doi.org/10.1101/2023.12.31.573734">https://doi.org/10.1101/2023.12.31.573734</a>) if you use this dataset in your research:</p> <p><code>Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E. Milkie, Joshua L. Lillvis, Alexander Kuhn, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N. Killilea, Eric Betzig, Srigokul Upadhyayula. Image processing tools for petabyte-scale light sheet microscopy data. bioRxiv 2023.12.31.573734; doi: <a href="https://doi.org/10.1101/2023.12.31.573734">https://doi.org/10.1101/2023.12.31.573734</a></code></p>
3D Reconstruction of Neuronal Allometry and Neuromuscular Projections in Asexual Planarians Using Expansion Tiling Light Sheet Microscopy dataset1
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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.