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123 results for “Light microscopy”
Interlaboratory study: Testing reproducibility of solid biofuels component identification using reflected light microscopy
<p><strong>Submitted data was used to write an article: </strong>Drobniak, A., Mastalerz, M., Jelonek, Z., Jelonek, I., Adsul, T., Andolšek, N., Ardakani, O.H., Congo, T., Demberelsuren, B., Donohoe, B.S., Douds, A., Flores, D., Ganzorig, R., Ghosh, S., Gize, A., Goncalves, P.A., Hackely, P., Hatcherian, J., Hower, J.C., Kalaitzidis, S., Kędzior, S., Knowles, W., Kuś, J., Lis, K., Lis, G., Liu, B., Luo, Q., Du, M., Mishra, D., Misz-Kennan, M., Mugerwa, T., O'Keefe, J., Park, J., Pearson, R., Petersen, H., Reyes, J., Ribeiro, J., Niedzwiedzkas, J.L., de la Rosa Rodriguez, G., Sosnowski, P., Valentine, B., Varma, A., Wojtaszek-Kalaitzidi, M., Xu, Z., Zdravkov, A., Ziemianin, K., Interlaboratory study: Testing reproducibility of biomass fuels component identification using reflected light microscopy. International Journal of Coal Geology 277, 104331. <a href="https://doi.org/10.1016/j.coal.2023.104331">https://doi.org/10.1016/j.coal.2023.104331</a>.</p> <p> </p> <p><strong>Funding acknowledgments: </strong>The project is co-financed by the Polish National Agency for Academic Exchange within the Polish Returns Programme (BPN/PPO/2021/1/00005/DEC/1), the National Science Center, Poland (2022/01/1/ST10/00024), and the research activities co-financed by the funds granted under the Research Excellence Initiative of the University of Silesia in Katowice, Poland. </p> <p> </p> <p><strong>Article Abstract: </strong>Considering global market trends and concerns about climate change and sustainability, increased biomass use for energy is expected to continue. As more diverse materials are being utilized to manufacture solid biomass fuels, it is critical to implement quality assessment methods to analyze these fuels thoroughly. One such method is reflected light microscopy (RLM), which has the potential to complement and enhance current standard testing, leading to improving fuel quality assessment and, ultimately, preventing avoidable air pollution. An interlaboratory study (ILS) was conducted to test the reproducibility of biomass fuels component identification using a reflected light microscopy technique. The exercise was conducted on thirty photomicrographs showing biomass and various undesired components (like plastics or mineral matter), which were purposely added (by the ILS organizers) to contaminate wood pellets and charcoal-based grilling fuels. Forty-six participants had various levels of difficulty identifying the marked components, and as a result, the percentage of correct answers ranged from 52.2 to 94.4%. Among the most difficult components to distinguish were petroleum products and inorganic matter. Various reasons led to the misidentification, including insufficient morphological descriptions of the components provided to participants, ambiguities of the nomenclature, limitations of the analytical and exercise method, and insufficient experience of the participants. Overall, the results indicate that RLM has the potential to enhance the quality assessment of biomass fuels. However, they also demonstrate that the petrographic classification used in this exercise requires further refinement before it can be standardized. While a new simplified classification of solid biomass fuels components was created as an outcome of this study, future research is necessary to refine the nomenclature, develop a microscopic morphological description of the components, and verify the accuracy of component identification with a follow-up ILS.</p>
Raw Data on Extracellular Particles in 613 Human and 163 Canine Diluted Plasma and Blood Samples Assessed by Interferometric Light Microscopy
<p><span>Extracellular nanoparticles (EPs) are cellular fragments. After being released in cell exterior, they become mediators of the cell-cell interaction. Their characterization in bodily fluids may reflect the clinical status of the organism. Here we present data on the number density <em>n</em> and hydrodynamic diameter <em>D</em><sub>h </sub>of EPs assessed directly in diluted plasma and blood by using a recently developed technique, Interferometric Light Microscopy (Romolo et al., 2022). The data are presented in the attached Table. </span></p> <p><span>We collected 613 blood and plasma samples from human patients with Inflammatory Bowel Disease (IBD) taken into tubes with trisodium citrate and ethylenediaminetetraacetic acid (EDTA) anticoagulants and 163 blood and plasma samples from canine patients with Brachycephalic Obstructive Airway Syndrome (BOAS). </span><span>The human study was conducted in accordance with the Declaration of Helsinki, and approved by the National Medical Ethics Committee of the Republic of Slovenia (0120-271/2022/4; KME 27 July 2022). All procedures in the animal study complied with the relevant Slovenian government regulations (Animal Protection Act, Official Gazette of the Republic of Slovenia, No. 43/2007). The animal study was approved by the Animals in Experiments Welfare Commission of the Veterinary Faculty, University of Ljubljana, approval number 18-3/2022-1. </span><span>Information regarding sample preparation is documented in the MIBlood-EV reports.</span></p> <div> <div> <div><span><a name="_msocom_1"></a></span></div> </div> </div>
Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: datasets collected using light microscopy and DNA metabarcoding
<p>This dataset contains all data required to reproduce the analyses conducted in Macgregor <em>et al. </em>(2018), using the R Notebook archived at doi: <a href="https://dx.doi.org/10.5281/zenodo.1322712">10.5281/zenodo.1322712</a>.</p> <p>Specifically, the dataset contains details of pollen transport detected on two matched samples, each containing 311 moths of 41 species, using two methods: a traditional light microscopy approach and a novel DNA metabarcoding approach. Both raw and manually-curated versions of each dataset are archived for full clarity. The dataset additionally contains all metadata required to fully interpret these data, including the RGB tables used to prepare Fig 4 in Macgregor <em>et al. </em>(2018).</p> <p>Macgregor <em>et al. </em>(2018) Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using light microscopy and DNA metabarcoding. <em>Ecological Entomology</em>, doi: <a href="https://dx.doi.org/10.1111/een.12674">10.1111/een.12674</a>.</p>
Dataset: Correlative Light, Electron Microscopy and Raman Spectroscopy Workflow to Detect and Observe Microplastic Interactions with Whole Jellyfish
<p>ABSTRACT</p> <p>Many researchers have turned their attention to understanding microplastic interaction with marine fauna. Efforts are being made to monitor exposure pathways and concentrations, and to assess the impact such interactions may have. To answer these questions, it is important to select appropriate experimental parameters and analytical protocols. This study focuses on medusae of <em>Cassiopea andromeda</em> jellyfish: a unique benthic jellyfish known to favor (sub-)tropical coastal regions which are potentially exposed to plastic waste from land-based sources. Juvenile medusae were exposed to fluorescent poly(ethylene terephthalate) and polypropylene microplastics (< 300 µm), resin embedded, and sectioned before analysis with confocal laser scanning microscopy as well as transmission electron microscopy and Raman Spectroscopy. Results show the fluorescent microplastics were stable enough to be detected with the optimized analytical protocol presented, and that their observed interaction with medusae occurs in a manner which is likely driven by the microplastic properties (<em>e.g.</em> density, hydrophobicity).</p>
ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy
<p>Data for submission to Wellcome Open Research entitled "ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy".</p> <p>Data_ultraLM.tif is an image stack from the fluorescence microscope mounted on the ultramicrotome.</p> <p>Data_miniLM.tif is an image stack from the fluorescence microscope mounted in the SBF-SEM.</p> <p>Data_miniLM_EM.tif is an image stack from the SBF-SEM while the miniLM was in-situ.</p>
Fig. 6 in Stereoscopic light-microscopy in biology - A review
Fig. 6: Stereoscopic images of an amoeba with its irregular pseudopodia extending into all spatial directions (width: 150 µm, single images: Wim van Egmond).
Fig. 5 in Stereoscopic light-microscopy in biology - A review
Fig. 5: Stereo-pair showing the freshwater polyp Hydra sp. under the light-microscope (height: 0.5 mm).
Fig. 3 in Stereoscopic light-microscopy in biology - A review
Fig. 3: Stereoscopic photographs of the trumpet animal Stentor sp, representing a sessile freshwater organism with partly massive occurrence (height: 200 µm, single images: Wim van Egmond).
Fig. 1 in Stereoscopic light-microscopy in biology - A review
Fig. 1: "Classical" methods of stereo-pair production which are described in detail in the scientific literature: (a) horizontal displacement of the object, (b) rotation of the object, (c) variation of the focus plane (restricted to transparent objects).
Fig. 4 in Stereoscopic light-microscopy in biology - A review
Fig. 4: Stereoscopic images of a triangular diatom which represents a widely distributed unicellular organism of small freshwater habitats with sumptuous stock of submerged vegetation (width: 250 µm, single images: Wim van Egmond).
Fig. 2 in Stereoscopic light-microscopy in biology - A review
Fig. 2: Main windows of the computer program PICOLAY which was developed for the generation of stereoscopic images from single photographs: (a) input window, (b) output window with generation of the object-depth map.
Fig. 7 in Stereoscopic light-microscopy in biology - A review
Fig. 7: Stereoscopic view on the multicellular green alga Volvox sp. (diameter: 250 µm, single images: Wim van Egmond).
Broca's Area Light-Sheet Microscopy
<p>Example dataset containing light-sheet selective plane illumination microscopy (SPIM) data to illustrate BIDS convention.<br> BIDS version 1.7.0</p>
(10)-Strobl2022A-DS0008 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0008 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(10)-Strobl2022A-DS0004 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0004 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(10)-Strobl2022A-DS0001 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0001 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(10)-Strobl2022A-DS0003 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0003 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(10)-Strobl2022A-DS0002 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0002 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(10)-Strobl2022A-DS0007 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0007 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
(10)-Strobl2022A-DS0009 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(10)-Strobl2022A-DS0009 – <em>Ceratitis capitata</em> TREhs43-hid<sup>Ala5</sup>_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
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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.