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37 results for “Optical microscopy”
Confocal Microscopy Visualizes Particle-Crack Interactions in Epoxy Composites with Optical Force Probe-Crosslinked Rubber Particles
<p>Data (*.csv and *.lif) corresponding to Figures 2-7 of the manuscript and Figures S1-S2 of the Supporting Information.</p>
Supplementary material - Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells
<p>Supplementary material containing the data used in the manuscript "Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells"</p>
Datasets for Background and Shading Correction of Optical Microscopy Images by BaSiC -- Downsampled Version
<p>This repository holds downsampled example data for publication: "<strong>A BaSiC tool for background and shading correction of optical microscopy images, Nature Communications (2017)</strong>" DOI: <a href="https://doi.org/10.1038/ncomms14836">https://doi.org/10.1038/ncomms14836</a>. For full-resolution testing data, please refer to Zenodo repository at DOI: <a href="https://zenodo.org/record/6334810#.YvD6zHZBxD8">10.5281/zenodo.6334810</a>.</p>
Data supporting publication: Revealing Mode Formation in Quasi-Bound States in the Continuum Metasurfaces via Near-Field Optical Microscopy
<p>This repository includes the data corresponding to the figures shown in the journal article entitledRevealing Mode Formation in Quasi-Bound States in the Continuum Metasurfaces via Near-Field Optical Microscopy, published in Advanced Materials on 02.08.2024</p>
Single Particle Investigation of Triolein Digestion using Optical Manipulation, Polarized Video Microscopy, and SAXS
<p>Hypothesis: Understanding how soft colloids, such as food emulsion droplets, transform based on their environment is critical for various applications, including drug and nutrient delivery and biotechnology. However, the mechanisms behind colloidal transformations within individual oil droplets still need to be better understood.</p> <p>Experiments: This study employs optical micromanipulation with microfluidics and polarized optical video microscopy to investigate the pancreatic lipase- and pH-triggered colloidal transformations in a single triolein droplet. Small-angle X-ray scattering (SAXS) provides complementary statistical insights and allows for detailed structural assignment.</p> <p>Findings: Optical video microscopy recorded the transformation of individual triolein emulsion droplets, with the smooth surface of these spherical particles becoming rough and the entire volume eventually being affected. The polarized microscopy revealed the coexistence of at least two distinct structures in a single particle during digestion, with their ratio and distribution altered by pH. The SAXS analysis assigned the optical anisotropy to emulsified inverse hexagonal- and multilamellar phases, coexisting with isotropic structures such as the micellar cubic phase. These results can help understand the liquid-liquid crystalline phase transformations inside an emulsion droplet and guide the design of advanced food emulsions.</p>
refering rawdata and code of "Ultrahigh-throughput single-pixel complex-field microscopy with frequency-comb acousto-optic coherent encoding (FACE)"
<p>Corresponding raw data and codes that produce all relative video and imaging results for real-time monitoring the physicochemical phenomena of microfluidics, microorganism's group, and chemical reactions, supporting and verifying the research article "Ultrahigh-throughput single-pixel complex-field microscopy with frequency-comb acousto-optic coherent encoding (FACE)".</p>
Datasets for Background and Shading Correction of Optical Microscopy Images by BaSiC
<p>This repository holds all the example data for publication: "<strong>A BaSiC tool for background and shading correction of optical microscopy images, Nature Communications (2017)</strong>" DOI: <a href="https://doi.org/10.1038/ncomms14836">https://doi.org/10.1038/ncomms14836</a>. A downsampled version is available at Zenodo repository with DOI: <a href="https://zenodo.org/record/6974039#.YvD8G3ZBxD8">10.5281/zenodo.6974039</a>.</p>
Dataset of "Challenging Point Scanning across Electron Microscopy and Optical Imaging using Computational Imaging"
<p>Dataset containing the jupyter notebook with codes for the simulation of the structured illumination patterns used for image reconstruction (the simulation parameters have been optimized to make sure that the patterns were almost identical to the experimental ones), the reconstruction algorithms. Moreover, there are three experimental dataset saved as txxt file, where each line contains the six biases applied to the electron modulator and the intensity measured by the single pixel detector that we used.</p>
Dataset of "Near-real-time diagnosis of electron optical phase aberrations in scanning transmission electron microscopy using an artificial neural network"
<p>Dataset containing the jupyter notebook used to construct the database of image, to model and train ANN and to analyze the experimental data. Furthermore there are also a reduced database of 100 images that can be utilized to test the ANN, the h5 file containing the ANN weigths and other supporting files.</p>
A Multimodal Dataset on Stainless Steel for Electrochemical Corrosion Studies: Optical Microscopy and Linear Sweep Voltammetry
<p>The upload includes optical and electrochemical data for corrosion experiments.</p> <p>This dataset presents the results of an experimental study conducted to investigate the electrochemical behavior of electropolished Stainless Steel 316L (SS316L) samples immersed in NaCl solutions. The combination of Linear Sweep Voltammetry (LSV) and optical microscopy techniques was employed to gather comprehensive insights into the electrochemical processes occurring on the surface of the stainless steel samples.</p> <p>The samples used in the experiment were electropolished SS316L, chosen for its widely recognized corrosion resistance properties and frequent application in various industrial sectors. LSV was performed on the samples in a potential range of -0.5V to 1.35V, (vs 3.4M KCl Ag/AgCl). NaCl solutions with concentrations of 5mM, 10mM, and 50mM were prepared to simulate different electrolyte conditions.</p> <p>Two different scan rates, 50mV/s and 100mV/s, were applied during the LSV experiments to observe the effect of varying scan rates on the electrochemical behavior of the SS316L samples. The scan rates were chosen to cover a range commonly encountered in electrochemical studies.</p> <p>List of experiments:</p> <ul> <li> 5 mM solution, 100mV/s scan rate</li> <li> 10 mM solution, 50mV/s scan rate</li> <li> 10 mM solution, 100mV/s scan rate</li> <li> 50 mM solution, 50mV/s scan rate</li> <li> 50 mM solution, 100mV/s scan rate</li> </ul> <p>The dataset is accompanied by animated plots. The top left plot shows electrochemistry data, bottom left - average normalized intensity and derivative of intensity. Top right - original optical images, bottom right - normalized images.</p> <p>The scale for optical images: 1px = 480 nm. Axes on images are in pixels</p> <p>Jupyter notebook with the code, used to create videos included. We recommend opening the Jupyter notebook file in a Python 3 environment.<br> </p>
Data from: Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy
<p>This repository contains the raw data of the experimental ISM dataset used to make the figures and supplementary figures for the paper entitled <em>Structured Detection for Simultaneous Super-Resolution and Optical Sectioning in Laser Scanning Microscopy.<br></em></p>
OSBM: Optical sectioning of unlabeled samples using bright-field microscopy
<p>This includes the FIJI macro and the image stack dataset used in the manuscript "Optical sectioning of unlabeled samples using bright-field microscopy".</p>
Label-free adaptive optics single-molecule localization microscopy for whole zebrafish
<p>The specimen-induced aberration has been a major factor limiting the imaging depth of single-molecule localization microscopy (SMLM). Here, we report the application of label-free wavefront sensing adaptive optics to SMLM for deep-tissue super-resolution imaging. The proposed system measures complex tissue aberrations from intrinsic reflectance rather than fluorescence emission and physically corrects the wavefront distortion more than three-fold stronger than the previous limit. This enables us to resolve sub-diffraction morphologies of cilia and oligodendrocytes in whole zebrafish as well as dendritic spines in thick mouse brain tissues at the depth of up to 102 μm with localization number enhancement by up to 37 times and localization precision comparable to aberration-free samples. The proposed approach can expand the application range of SMLM to whole zebrafish that cause the loss of localization points owing to severe tissue aberrations.</p>
High-speed TIRF and 2D super-resolution structured illumination microscopy with large field of view based on fiber optic components
<p>Super-resolved structured illumination microscopy (SR-SIM) is among the most flexible, fast, and least perturbing fluorescence microscopy techniques capable of surpassing the optical diffraction limit. Current custom-built instruments are easily able to deliver two-fold resolution enhancement at video-rate frame rates, but the cost of the instruments is still relatively high, and the physical size of the instruments based on the implementation of their optics is still rather large. Here, we present our latest results towards realizing a new generation of compact, cost-efficient, and high-speed SR-SIM instruments. Tight integration of the fiber-based structured illumination microscope capable of multi-color 2D- and TIRF-SIM imaging, allows us to demonstrate SR-SIM with a field of view of up to 150 × 150 μm<sup>2</sup> and imaging rates of up to 44 Hz while maintaining highest spatiotemporal resolution of less than 100 nm. We discuss the overall integration of optics, electronics, and software that allowed us to achieve this, and then present the fiberSIM imaging capabilities by visualizing the intracellular structure of rat liver sinusoidal endothelial cells, in particular by resolving the structure of their trans-cellular nanopores called fenestrations.</p>
Supplementary material - Label-free multimodal nonlinear optical microscopy reveals hallmarks of bone composition in pathophysiological conditions
<p>The repository features Excel worksheets including all the data used through this work and reported in the manuscript figures and graphs. More precisely, we included the following: </p> <ul> <li>Figure 4. SHG intensity values measured from WT and KO murine spines counterparts, both in parallel and orthogonal light polarization with respect to the craniocaudal axis of the vertebrae.</li> <li>Figure 5A. Quantization of ColIa1 gene expression level after mRNA extraction from WT and Dpp3 KO mice.</li> <li>Figure 5B. Absorbance values at 540 nm after Sirius Red staining of primary osteoblast isolated from WT and Dpp3 KO neonatal calvaria, used to assess and compare the in-vitro collagen production of the two murine models.</li> <li>Figure 7. SRS intensity ratios measured between bone and bone marrow regions of WT and Dpp3 KO models, both at the 2850 cm-1 Raman mode of CH2 stretching in lipids and at the 2920 cm-1 Raman mode of CH3 stretching in proteins.</li> <li>Figure 8. Data of gene expression analysis of selected genes relevant for lipid transport, uptake, and metabolism (i.e., CD 36, Fabp4, Lrp1, Fatp1, PGC1, CPT1, Pex7 and Glut1), in the flushed bone of WT and Dpp3 KO mice.</li> </ul>
FIGURES 13–14. Congocepheus ornatus Mahunka 1983. Adult female. Optical microscopy. 13 in Revision of the family Carabodidae (Acari: Oribatida) V (Fifth part). Redescription of Congocepheus latilamellatus Mahunka 1984, with complementary studies of C. ornatus, Mahunka 1983. Descriptions of Tanzaniacepheus gen. nov. and Zimbabwecepheus gen. nov.
FIGURES 13–14. Congocepheus ornatus Mahunka 1983. Adult female. Optical microscopy. 13. lateral view; 14. posterior view, inclined to ventral. Abbreviations: see Material and Methods. Scale bars: 13 = 170 µm; 14 = 150 µm.
FIGURES 8–12. Congocepheus latilamellatus Mahunka 1984. Optical microscopy. 8 in Revision of the family Carabodidae (Acari: Oribatida) V (Fifth part). Redescription of Congocepheus latilamellatus Mahunka 1984, with complementary studies of C. ornatus, Mahunka 1983. Descriptions of Tanzaniacepheus gen. nov. and Zimbabwecepheus gen. nov.
FIGURES 8–12. Congocepheus latilamellatus Mahunka 1984. Optical microscopy. 8. adult female, lateral view; 9. leg I, antiaxial view; 10. leg II, antiaxial; 11. leg III, antiaxial; 12. leg IV antiaxial. Abbreviations: see Material and Methods. Scale bars: 8 = 65 µm; 9–12 = 100µm.
FIGURES 1–7. Congocepheus latilamellatus Mahunka 1984. Optical microscopy. 1 in Revision of the family Carabodidae (Acari: Oribatida) V (Fifth part). Redescription of Congocepheus latilamellatus Mahunka 1984, with complementary studies of C. ornatus, Mahunka 1983. Descriptions of Tanzaniacepheus gen. nov. and Zimbabwecepheus gen. nov.
FIGURES 1–7. Congocepheus latilamellatus Mahunka 1984. Optical microscopy. 1. dorsal view; 2. anterior prodorsal zone, inclined; 3. anterior zone of lamellae; 4. pedotecta I and II, lateral view; 5. anterior zone of prodorsum, inclined to posterior; 6. pedotecta I–II, anteroposterior view; 7. pedotecta I–II, with a large degree of inclination, anteroposterior view. Abbreviations: see Material and Methods. Scale bars: 1 = 175 µm; 2 = 110µm; 4, 5, 6, 7 = 30µm.
Quantitative measures of corneal transparency, derived from objective analysis of depth-resolved corneal images, demonstrated with full-field optical coherence tomographic microscopy
<p>Supporting data for: <a href="https://zenodo.org/record/2579947">Quantitative measures of corneal transparency, derived from objective analysis of depth-resolved corneal images, demonstrated with full-field optical coherence tomographic microscopy</a></p>
Dataset for publication 'Automated g-ratio calculation of sciatic nerve bundles in mice – a new approach for optical microscopy '
<p>Dataset corresponding to the publication <strong>Automated g-ratio calculation of sciatic nerve bundles in mice – a new approach for optical microscopy</strong> intended for publication at Nature Scientific Reports. This repository contains the training, validation and test data.</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.