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42 results for “serial sectioning”
Seroprevalence of IgG antibodies against SARS coronavirus 2 in Belgium – a serial prospective cross-sectional nationwide study of residual samples (March – October 2020)
<p>This dataset contains information on seven prospective cross-sectional nationwide residual sera collection rounds. The samples were analyzed for IgG antibodies against S1 proteins of SARS-CoV-2 with a semi-quantitative commercial ELISA (EuroImmun, Luebeck, Germany).</p> <p>We provide a CSV file containing the following variables:</p> <ul> <li><strong>code</strong>: unique sample code</li> <li><strong>age_cat</strong>: age categories by 10-year age bands (0-10, 10-20, ..., 80-90, 90-Inf), the lower limit is included, e.g. 0-10 = [0,10)</li> <li><strong>sex</strong>: sex (f = female, m = male)</li> <li><strong>province</strong>: province of residence (11 categories)</li> <li><strong>region</strong>: region of residence (3 categories: Brussels, Flanders, Walloon)</li> <li><strong>collection_round</strong>: collection round (values 1 to 7)</li> <li><strong>collection_start</strong>: start date of the collection round</li> <li><strong>collection_end</strong>: end date of the collection round</li> <li><strong>igg_orig</strong>: measured IgG OD value as character (note, a semi-quantitative ELISA was used, i.e. this should not be interpreted continiously)</li> <li><strong>igg_cat</strong>: categorized IgG OD values <ul> <li><em>LoD</em>: IgG OD < 0.15</li> <li><em>negative</em>: 0.15 ≤ IgG OD < 0.8</li> <li><em>borderline</em>: 0.8 ≤ IgG OD < 1.1</li> <li><em>positive</em>: 1.1 ≤ IgG OD</li> </ul> </li> </ul> <p>Please see publication mentioned underneath for more details (<a href="https://doi.org/10.1101/2020.06.08.20125179">https://doi.org/10.1101/2020.06.08.20125179</a>).</p> <p><strong>Funding:</strong> This work received funding from the European Union's Horizon 2020 research and innovation program - project EpiPose (No 101003688), the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 682540 TransMID), the Flemish Research Fund (FWO 1150017N) and from The Antwerp University Fund; which is a community of donors who contribute to research and education with their personal commitment through a donation, gift, bequest or through academic chairs. The funders had no role in study design, data collection, data analysis, data interpretation, writing or submitting of the report. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication.</p>
Serial section images of Oikopleura dioica juvenile using SBF-SEM
<p>The larvacean, <i>Oikopleura dioica</i> is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form. The dataset is serial section images of Oikopleura dioica juvenile that were obtained using SBF-SEM (Serial block face scanning electron microscopy). The 1961 TIFF images were compressed to a zip file.</p> <p>The juveniles were fixed at 10.5 hours post fertilization, 30 min after the tail shift (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The dataset would be used as a basic morphological data of this animal to explore organ structures and cellular composition at electron microscopic level.</p> <p>This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (Scientific Reports, 2021, 11, 4833) (https://www.nature.com/articles/s41598-021-83706-y)</p>
Serial Coronal Sections Of An Adult Mouse Brain - Sample Dataset
<p>Experimental data: serial coronal sections of the brain of an adult mouse.</p> <p>20 um brain sections sampled every 80 um, imaged on an Olympus VS120 slide scanners with a 10x objective</p> <p>Contains label and overview images and 3 fluorescent channels:</p> <ul> <li>DAPI channel, cell nuclei</li> <li>FITC channel, autofluorescence</li> <li>Cy3 channel, fluorescent sparse mCherry labelled cells</li> </ul> <p>This dataset can be used as a test dataset for the <a href="https://biop.github.io/ijp-imagetoatlas/">Aligning Big Brain and Atlases</a> tool.</p> <p>Animal handling according to protocols approved by the Swiss animal license VD2808.2</p> <p>Two zipped QuPath project that are using the OMERO extension are also provided. One contains the full 97 section dataset, one contains a subset of 25 sections. These data are present in the German BioImaging public OMERO instance (<a href="https://omero-tim.gerbi-gmb.de">https://omero-tim.gerbi-gmb.de</a>).</p> <p> </p> <p> </p>
FIG. 31. Hsiangolestes youngi, IVPP V7438, serial sections 9–49 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships
FIG. 31. Hsiangolestes youngi, IVPP V7438, serial sections 9–49 (from back forward).
FIG. 30. Hsiangolestes youngi, IVPP V7438, serial sections 50–80 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships
FIG. 30. Hsiangolestes youngi, IVPP V7438, serial sections 50–80 (from back forward).
FIG. 29. Hsiangolestes youngi, IVPP V7438, serial sections 85–115 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships
FIG. 29. Hsiangolestes youngi, IVPP V7438, serial sections 85–115 (from back forward).
FIG. 28. Hsiangolestes youngi, IVPP V7438, serial sections 234–257 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships
FIG. 28. Hsiangolestes youngi, IVPP V7438, serial sections 234–257 (from back forward).
FIG. 26. Hsiangolestes youngi, IVPP V7438, serial sections 283–331 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships
FIG. 26. Hsiangolestes youngi, IVPP V7438, serial sections 283–331 (from back forward).
FIG. 27. Hsiangolestes youngi, IVPP V7438, serial sections 260–278 in Cranial And Postcranial Morphology Of The Insectivoran-Grade Mammals Hsiangolestes And Naranius (Mammalia, Eutheria) With Analyses Of Their Phylogenetic Relationships
FIG. 27. Hsiangolestes youngi, IVPP V7438, serial sections 260–278 (from back forward).
Serial section images of Oikopleura dioica juvenile using SBF-SEM
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Data from: Serial-section atlas of the Tritonia pedal ganglion
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Serial section images of Oikopleura dioica larva using SBF-SEM
<p>The larvacean, Oikopleura dioica is a planktonic chordate, which is an emerging model organism with short life cycle of 5 days and belongs to tunicates (urochordates). Organ formation in the trunk proceeds in seven hours form hatching of tailbud larvae at three hours after fertilization (hpf) to completion of organ formation in fully functional juveniles that start feeding at 10 hpf and are just miniature of adult form. The dataset is serial section images of Oikopleura dioica juvenile that were obtained using SBF-SEM (Serial block face scanning electron microscopy). The 1812 TIFF images were compressed to a zip file.</p> <p>The larva were fixed at 3 hours post fertilization, 10 min after hatching (Nishida, H., 2008 Development of the appendicularian Oikopleura dioica: culture, genome, and cell lineages. Dev. Growth Differ. 50, S239–S256.). The dataset would be used as a basic morphological data of this animal to explore organ structures and cellular composition at electron microscopic level.</p> <p>This data is related to the paper, 3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. (Scientific Reports, 2021, 11, 4833) (https://www.nature.com/articles/s41598-021-83706-y).</p>
Test dataset for "Spatial Integration of Multi-Omics Data from Serial Sections using the novel Multi-Omics Imaging Integration Toolset"
<p>The uploaded tar file contains anonymized and reduced test data for the paper "Spatial Integration of Multi-Omics Data from Serial Sections using the novel Multi-Omics Imaging Integration Toolset". (doi: https://doi.org/10.1101/2024.06.11.598306; https://github.com/mwess/miit)</p> <p>Dataset description:<br>- 9 serial histology sections with the following stains: (HES, HE, HES, HES, HES, MTS, IHC, IHC, HES)<br>- Sections are indexed in the following way (due to some sections not being part of this project): 1,2,3,6,7,8,9,10,11<br>- Each serial section contains: <br> - landmarks with matching labels across all sections.<br> - semi-manually generated tissue masks <br>- Section 2 contain spatial transcriptomics data and one annotation file in geojson format.<br>- Sections 6 and 7 contain imzml data that were generated with MALDI-MSI in positive ion mode (section 6) and negative ion mode (section 7) and additional histology annotations.<br>- MALDI-MSI is reduced. The positive ion data contains only intensities and spectra for spermine. The negative ion mode data contains only intensities and spectra for citrate and zinc.<br>- ST data contains only locations of spots and scalefactors. (I.e. no count data is included.). Barcode ids are randomly generated. <br>- In addition, for each ST spot histopathological annotations and GSEA scores for the Citrate-Spermine Secretion gene signature are provided.</p> <p>Abbreviations:</p> <p>- HES = Hematoxylin-Erythrosine-Saffron<br>- HE = Hematoxylin-Eosin<br>- MTS = Masson's Trichrome Staining<br>- IHC = Immunohistochemistry<br>- ST = Spatial Transcriptomics, here refers to Visium10X arrays.<br>- MALDI-MSI = Matrix-Assisted Laser Desorption Ionization - Mass Spectrometry Imaging.</p> <p> </p>
Serial thin section movie of every third section from the DTC to the distal extensions of Sh1 in a young adult hermaphrodite posterior gonad arm
<p>Gap-junctional signaling mediates myriad cellular interactions in metazoans. Yet, how gap junctions control the positioning of cells in organs is not well understood. Innexins compose gap junctions in invertebrates and affect organ architecture. Here, we investigate the roles of gap-junctions in controlling distal somatic gonad architecture and its relationship to underlying germline stem cells in <em>Caenorhabditis elegans</em>. We show that a reduction of soma-germline gap-junctional activity causes displacement of distal sheath cells (Sh1) towards the distal end of the gonad. We confirm, by live imaging, transmission electron microscopy, and antibody staining, that bare regions – lacking somatic gonadal cell coverage of germ cells – are present between the distal tip cell (DTC) and Sh1, and we show that an innexin fusion protein used in a prior study encodes an antimorphic poisonous gap junction subunit that mispositions Sh1. We determine that, contrary to the model put forth in the prior study based on this fusion protein, Sh1 mispositioning does not markedly alter the position of the borders of the stem cell pool nor of the progenitor cell pool. Together, these results demonstrate that gap junctions can control the position of Sh1, but that Sh1 position is neither relevant for GLP-1/Notch signaling nor for the exit of germ cells from the stem cell pool.</p>
Microscopic serial sectioning of a half steel-steel clinch joint
<p>(Specimen ID: B02_SS_CV_003) </p> <p>This data contains 68 high-resolution images of different planes of a half clinch joint, 1 CSV file with the metadata and 1 GIF with all images. The z-spacing of the planes can be taken from the .csv file. The clinch joint was made of a 1.5 mm thick HCT590X+Z steel plate with a 5 mm diameter conical punch (A50100) and an 8 mm fixed round die (DB8016) from TOX®. </p> <p>Founding<br> Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – TRR 285 – Project-ID 418701707</p>
Study of Breast Cancer Shrinkage Modes After Neoadjuvant Chemotherapy With Whole-mount Serial Sections and Three-dimensional Pathological and MRI Reconstruction
ClinicalTrials.gov study NCT01917578. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Serial section images of Oikopleura dioica larva using SBF-SEM
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Serial thin section movie of every third section from the DTC to the distal extensions of Sh1 in a young adult hermaphrodite posterior gonad arm
Open the record for dataset details and reuse information.
FIG. 4. — Serial cross sections from below upwards through a in Comparative floral anatomy of some species of Brassicaceae and its taxonomic significance
FIG. 4. — Serial cross sections from below upwards through a floral bud of Brassica oleracea L. showing: A, pedicel vasculature; continuous siphonostele; B-F, calyx vasculature; four sepal median bundles arise from sepal-median-nectarial complexes; D-F, corolla vasculature; from petal-sepal marginal-nectarial complexes; D-G, androecium vasculature; six staminal bundles to six fertile stamens emerge directly from the central stele; H-N, gynoecium vasculature; four vascular masses, two dorsal carpellary bundles and two ventral carpellary masses. Scale bar: 500 μm.
Data from: Reconstruction of genetically identified neurons imaged by serial-section electron microscopy
Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identified neurons, and developed a protocol that enhances the electron-density of the labeled cells and while retaining quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that dramatically speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by at least two orders of magnitude, facilitating directed inquiry of circuit motifs.
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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.