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28 results for “structured illumination”
Example Microscopy Metadata JSON files produced using Micro-Meta App to document the acquisition of example images using a custom-built TIRF Epifluorescence Structured Illumination Microscope
<p><strong>Example Microscopy Metadata JSON files produced using the <a href="https://wu-bimac.github.io/MicroMetaApp.github.io/">Micro-Meta App</a> documenting an example raw-image file acquired using the custom-built TIRF Epifluorescence Structured Illumination Microscope.</strong></p> <p>For this use case, which is presented in Figure 5 of <a href="http://doi: https://doi.org/10.1101/2021.05.31.446382">Rigano et al., 2021</a>, Micro-Meta App was utilized to document:</p> <p>1) The <strong>Hardware Specifications</strong> of the custom build TIRF Epifluorescence Structured light Microscope (TESM; <a href="https://www.pnas.org/content/109/8/E471.long">Navaroli et al., 2010</a>) developed, built on the basis of the based on Olympus IX71 microscope stand, and owned by the Biomedical Imaging Group (http://big.umassmed.edu/) at the Program in Molecular Medicine of the University of Massachusetts Medical School. Because TESM was custom-built the most appropriate documentation level is <strong>Tier 3</strong> (<em>Manufacturing/Technical Development/Full Documentation</em>) as specified by the <a href="https://doi.org/10.5281/zenodo.4710731">4DN-BINA-OME</a> Microscopy Metadata model (<a href="https://doi.org/10.1101/2021.04.25.441198">Hammer et al., 2021</a>).</p> <p>The TESM Hardware Specifications are stored in: <strong>Rigano et al._Figure 5_UseCase_Biomedical Imaging Group_TESM.JSON</strong></p> <p>2) The <strong>Image Acquisition Settings</strong> that were applied to the TESM microscope for the acquisition of an example image (FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif) obtained by Nicholas Vecchietti and Caterina Strambio-De-Castillia. For this image, TZM-bl human cells were infected with HIV-1 retroviral three-part vector (FSWT+PAX2+pMD2.G). Six hours post-infection cells were fixed for 10 min with 1% formaldehyde in PBS, and permeabilized. Cells were stained with mouse anti-p24 primary antibody followed by DyLight488-anti-Mouse secondary antibody, to detect HIV-1 viral Capsid. In addition, cells were counterstained using rabbit anti-Lamin B1 primary antibody followed by DyLight649-anti-Rabbit secondary antibody, to visualize the nuclear envelope and with DAPI to visualize the nuclear chromosomal DNA.</p> <p>The Image Acquisition Settings used to acquire the FSWT-6hVirus-10minFIX-stk_4-EPI.tif.ome.tif image are stored in: <strong>Rigano et al._Figure 5_UseCase_AS_fswt-6hvirus-10minfix-stk_4-epi.tif.JSON</strong></p> <p><em><strong>Instructional video tutorials on how to use these example data files:</strong></em><br> Use these videos to get started with using Micro-Meta App after downloading the example data files available here.</p> <ul> <li><a href="https://vimeo.com/562022222">Part 1/2</a></li> <li><a href="https://vimeo.com/562022281">Part 2/2</a></li> </ul>
Data and code associated with "Spatial wavefront shaping with a nanostructured metasurface for structured illumination microscopy"
<p>Data and code associated with the manuscript "Spatial wavefront shaping with a nanostructured metasurface for structured illumination microscopy"</p>
FIGURE 7 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 7. Boxplot of Tukey HSD test illustrating three major length types (a–c) of single folded sperm packages in Scorpiones. Representatives of the three groups in boldface (see text).
Fully-Automated Multicolour Structured Illumination Module for Super-resolution Microscopy
<p> </p> <p>In the rapidly advancing field of biological imaging, high-resolution techniques that are cost-effective and accessible are essential for observing and understanding intracellular dynamics. Structured illumination microscopy (SIM) is a preferred method for achieving high axial and lateral resolution in living samples due to its optical sectioning and minimal phototoxicity. However, the high cost and complexity of conventional SIM systems limit their widespread use. In our work, we present an open-source, fully-automated, two-color structured illumination module that is compatible with commercially available microscope stands. The compact design, which includes low-cost single-mode fiber-coupled lasers and a digital micromirror device (DMD), is integrated into the open-source acquisition and control software ImSwitch to facilitate real-time super-resolution imaging. This system achieves up to a 1.55-fold improvement in lateral resolution compared to conventional wide-field microscopy. </p> <p>To ensure optimal DMD diffraction performance, we developed a model using tilt and roll pixels, enabling the use of low-cost video projectors in coherent SIM setups. Our aim is to democratize SIM-based super-resolution microscopy by providing comprehensive open-source documentation and a modular software framework compatible with various hardware components (e.g., cameras, stages) and reconstruction algorithms. </p> <p>All datasets generated and analyzed during this study are openly available and can be accessed through our public repository <a href="https://opensimmo.github.io/">[repository link]</a>. The datasets include raw and processed images, calibration files, and software scripts, enabling replication and further innovation. This approach will help upgrade as many devices as possible to the super-resolution realm, fostering greater accessibility and collaboration in the scientific community</p>
Video-rate multi-color structured illumination microscopy with simultaneous real-time reconstruction (Datasets)
<p>Raw data used for figures in the paper titled "Video-rate multi-color structured illumination microscopy with simultaneous real-time reconstruction"</p>
FIGURE 5 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 5. Sperm packages of Urodacidae Pocock, 1893 (A, B), Diplocentridae Karsch, 1880 (C, D), Scorpionidae Latreille, 1802 (E, F), and Bothriuridae Simon, 1880 (G–L) imaged with scanning electron microscopy (A–C, G, J) or light microscopy (D–F, H, I, K, L). A, B. Urodacus planimanus Pocock, 1893: ellipsoidal/ spherical. C. Diplocentrus lindo Stockwell and Baldwin, 2001: spiral/spherical. D. Nebo hierichonticus (Simon, 1872): bent. E. Pandinus imperator (C.L. Koch, 1841): straight. F. Scorpio fuliginosus (Pallary, 1928): ellipsoidal. G. Brachistosternus ferrugineus (Thorell, 1876): canelike. H. Brachistosternus pentheri Mello-Leitão, 1931: canelike. I. Lisposoma josehermana Lamoral, 1979: straight. J. Orobothriurus tamarugal Ochoa et al., 2011: straight. K. Rumikiru lourencoi (Ojanguren Affilastro, 2003): straight. L. Thestylus aurantiurus Yamaguti and Pinto-daRocha, 2003: straight. Scale bars: 25 µm.
FIGURE 4 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 4. Sperm packages of Chactidae Pocock, 1893 (A, B), Vaejovidae Thorell, 1876 (C–F), Heteroscorpionidae Kraepelin, 1905 (G, H), Hemiscorpiidae Pocock, 1893 (I), and Hormuridae Laurie, 1896 (J–L) imaged with scanning electron microscopy (A–J) or light microscopy (K, L). A, B. Uroctonus mordax Thorell, 1876: bent. C, D. Paravaejovis spinigerus (Wood, 1863): bent. E. Graemeloweus glimmei (Hjelle, 1972): bent. F. Vejovoidus longiunguis (Williams, 1969): bent. G, H. Heteroscorpion goodmani Lourenco, 1996: bent/double bent. I. Hemiscorpius lepturus Peters, 1861: bent. J. Hadogenes troglodytes (Peters, 1861): annular. K, L. Hormurus sp., Queensland, Australia: annular, double bent. Scale bars: 25 µm.
FIGURE 9 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 9. Schematic illustration summarizing the major types, shapes, and folding of sperm packages in Scorpiones with hypothesized evolutionary transformation from absence (free sperm), e.g., Buthida Soleglad and Fet 2003: A. Straight: fusiform, e.g., Parabuthus granulatus (Ehrenberg, 1831) (Buthidae C.L. Koch, 1837); straight, e.g., Iuridae Thorell, 1876, and Superstitioniidae Stahnke, 1940; or canelike, e.g., Bothriuridae Simon, 1880. B. Single fold: bent in half, e.g., Vaejovidae Thorell, 1876, Timogenes and Vachonia Abalos, 1954 (Bothriuridae). C. Multiple folds: ellipsoidal: double parallel fold, e.g., Tetratrichobothrius flavicaudis (De Geer, 1778), Nullibrotheas allenii (Wood, 1863); spiral, e.g., Euscorpiops longimanus (Pocock, 1893); double bent open gatefold, e.g., Broteochactas Pocock, 1893; annular: twisted, e.g., Hormuridae Laurie, 1896; or ringlike, e.g., Bothriurus Peters, 1861, and Timogenes Simon, 1880 (Bothriuridae).
FIGURE 1 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 1. Sperm packages of Bothriuridae Simon, 1880 (A, D, E, F), Superstitioniidae Stahnke, 1940 (B), Euscorpiidae Pocock, 1893 (C), and Buthidae C.L. Koch, 1837 (G–L), imaged with light microscopy (A–F) or scanning electron microscopy (G–L). A, D, E. Timogenes elegans (Mello-Leitão, 1931): bent, annular, straight. B. Superstitionia donensis Stahnke, 1940: straight. C. Tetratrichobothrius flavicaudis (De Geer, 1778): double bent/ellipsoidal; numbers represent folding that causes differences in shape. F. Brachistosternus ferrugineus (Thorell, 1876): straight. G. Zabius fuscus (Thorell, 1876): absent. H. Buthus paris (C.L. Koch, 1839): absent. I. Teruelius ankarana (Lourenço and Goodman, 2003): absent. J. Hottentotta conspersus (Thorell, 1876): absent. K. Babycurus jacksoni (Pocock, 1890): absent. L. Lychas obsti Kraepelin, 1913: absent. Arrows indicate folding of sperm packages described in text, including variations in conspecifics. Scale bars: 25 µm.
FIGURE 8 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 8. Transmission electron micrographs of spermatozoa from sperm packages of the bothriurid, Bothriurus bonariensis (C.L. Koch, 1842), sectioned at different points along an axis (A–D), and of sperm packages of four species of Bothriuridae Simon, 1880 sectioned in the middle (E–H). A. Head, middle piece, and flagella of different sperm packages. B. Nuclei of heads from different spermatozoa. C. Middle piece of different spermatozoa with paired mitochondria. D. Flagella of different spermatozoa. E. Bothriurus bonariensis. F. Timogenes elegans (Mello-Leitão, 1931). G. Brachistosternus ferrugineus (Thorell, 1876). H, I. Urophonius brachycentrus (Thorell, 1876). Inset in E–H illustrates details of axoneme. Abbreviations: axo, axoneme; f, flagellum; h, head; mit, mitochondria; mp, middle piece; n, nucleus. Scale bars: 0.5 µm (A–D); 2.5 µm (E–H).
FIGURE 3 in Bundles of Sperm: Structural Diversity in Scorpion Sperm Packages Illuminates Evolution of Insemination in an Ancient Lineage
FIGURE 3. Sperm packages of Caraboctonidae Kraepelin, 1905 (A, B), Superstitioniidae Stahnke, 1940 (C), Chactidae Pocock, 1893 (D–K), and Troglotayosicidae Lourenco, 1998 (L) imaged with scanning electron microscopy (A–C, E–G, K) or light microscopy (D, H–J, L). A. Caraboctonus keyserlingi Pocock, 1893: straight. B. Hadruroides lunatus (L. Koch, 1867): straight. C. Superstitionia donensis Stahnke, 1940: straight. D, E. Nullibrotheas allenii (Wood, 1863): ellipsoidal, double bent. F, G. Brotheas sp., Bartica District, Guyana: ellipsoidal, double bent. H. Broteochactas nitidus Pocock, 1893: double bent. I. Chactopsoides anduzei (González-Sponga, 1982): double bent. J. Chactas aequinoctialis (Karsch, 1879): ellipsoidal, spherical. K. Teuthraustes sp., Aguay Province, Ecuador: ellipsoidal. L. Troglotayosicus humiculum Botero-Trujillo and Francke, 2009: bent. Scale bars: 25 µm.
Raw ptychography data for manuscript with title 'Structured Illumination Ptychography and At-wavelength Characterization with an EUV diffuser at 13.5 nm Wavelength'
<p>- Given are the HDF files containing the raw diffraction patterns<br> - Although some meta-data might be available in these files, these might not be correct. The following data were used for reconstruction:<br> wavelength: 13.5 nm<br> distance sample <-> detector: ~29.2 mm<br> sCMOS pixel size: 11 um<br> Number of incoherent modes: 4<br> Initial probe guess: 9 um<br> For the reconstruction, OPR was used (Although it might have not been necessary for all data. However, to have comparable results it was used for each reconstruction)<br> - For each scenario, there are two data sets to calculate the Fourier ring correlation (FRC)<br> - For the analysis of the diffuser the reconstructed probe of the data set "dp_diffuser_max_dynam_range.hdf5" was used</p> <p>- Data were measured at the Institute of Applied Physics in Jena using a Fiber Laser driven High-order harmonic source</p> <p>Please contact me (wilhelm.eschen@uni-jena.de) for additional support.</p>
Data associated with "Robust Structured Illumination Microscopy with Bayesian Noise Control"
<p>Experimental and synthetic data saved in tiff and/or zarr formats and SIM reconstruction scripts written in Python (Wiener and FISTA-SIM0. These also include estimated SIM patterns which are needed for B-SIM</p><ul><li>Synthetic data consisting of variably spaced line pairs. Found in <a href="https://zenodo.org/uploads/10037823">2023_10_02_synthetic_line_pairs.zip</a></li><li>Experimental data. Fluorescence images of one of the variably spaced line pair patterns on an ArgoSIM calibration slide. Found in <a href="https://zenodo.org/uploads/10037823">2023_08_02_folder=002_argosim_slide.zip</a></li><li>Experimental data. MitoTracker Red labelled mitochondria in live HeLa cells. Found in <a href="2023_08_07_folder=011_mitos_live_hela.zip">2023_08_07_folder=011_mitos_live_hela.zip</a></li><li>Camera calibration maps, including gain, variance, and offset. Found in <a href="camera_calibration.zip">camera_calibration.zip</a></li></ul>
Deep, shallow and surface fault-zone deformation during and after the 2021 Mw7.4 Maduo, Qinghai, earthquake illuminates fault structural immaturity
<p>These datasets include the postseismic InSAR time series on ascending and descending tracks and the relocated aftershocks (Wang et al., 2021) of the 2021 Maduo earthquake. The details can be found in our JGR paper.</p> <p>Reference</p> <p>Wang, W., Fang, L., Wu, J., Tu, H., Chen, L., Lai, G., & Zhang, L. (2021). Aftershock sequence relocation of the 2021 Ms7. 4 Maduo earthquake, Qinghai, China. Science China Earth Sciences, 64(8), 1371-1380.</p>
Supplementary data for: Graphene Microelectrode Arrays, 4D Structured Illumination Microscopy, and a Machine Learning Spike Sorting Algorithm Permit the Analysis of Ultrastructural Neuronal Changes During Neuronal Signalling in a Model of Niemann-Pick Disease Type C
<p>Supplementary example data for the work presented in "<em>Graphene Microelectrode Arrays, 4D Structured Illumination Microscopy, and a Machine Learning Spike Sorting Algorithm Permit the Analysis of Ultrastructural Neuronal Changes During Neuronal Signalling in a Model of Niemann-Pick Disease Type C</em>". </p> <p><strong>Abstract: </strong></p> <p>Simultaneously recording network activity and ultrastructural changes of the synapse is essential for advancing our understanding of the basis of neuronal functions. However, the rapid millisecond-scale fluctuations in neuronal activity and the subtle sub-diffraction resolution changes of synaptic morphology pose significant challenges to this endeavour. Here, we use specially designed graphene microelectrode arrays (G-MEAs), which are compatible with high spatial resolution imaging across various scales as well as permit high temporal resolution electrophysiological recordings to address these challenges. Furthermore, alongside G-MEAs, we have developed an easy-to-implement machine learning algorithm to efficiently process the large datasets collected from MEA recordings. We demonstrate that the combined use of G-MEAs, machine learning (ML) spike analysis, and four-dimensional (4D) structured illumination microscopy (SIM) enables monitoring the impact of disease progression on hippocampal neurons which have been treated with an intracellular cholesterol transport inhibitor mimicking Niemann-Pick disease type C (NPC), and show that synaptic boutons, compared to untreated controls, significantly increase in size, leading to a loss in neuronal signalling capacity.</p> <p> </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>
Data from: Anatomy of an agricultural antagonist: Feeding complex structure and function of three xylem sap-feeding insects illuminated with synchrotron-based 3D imaging
Open the record for dataset details and reuse information.
Data from: The influence of illumination regimes on the structure of ant (Hymenoptera, Formicidae) community composition in urban habitats
Open the record for dataset details and reuse information.
Data from: Genomic data illuminates demography, genetic structure and selection of a popular dog breed
Open the record for dataset details and reuse information.
Micro-stepping Extended Focus reduces photobleaching and preserves structured illumination super-resolution features
<p><span>Despite progress made in confocal microscopy, even fast systems still have insufficient temporal resolution for detailed live cell volume imaging, such as tracking rapid movement of membrane vesicles in three-dimensional space. Depending on the shortfall, this may result in undersampling and/or motion artifacts that ultimately limit the quality of the imaging data. By sacrificing the detailed information in the Z-direction, we propose a new imaging modality that involves capturing fast "<i>projections</i>"<i> </i>from the field of depth which shortens imaging time by approximately an order of magnitude as compared to standard volumetric confocal imaging. With faster imaging, radiation exposure to the sample is reduced, resulting in less fluorophore photobleaching and potential photodamage. The implementation minimally requires two synchronized control signals that drive a piezo stage and trigger the camera exposure. The device generating the signals has been tested on spinning disk confocals and instant structured-illumination-microscopy (iSIM) microscopes. Our calibration images show that the approach provides highly repeatable and stable imaging conditions that enable photometric measurements of the acquired data, in both standard live imaging and super-resolution modes. </span></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)
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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.