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175 results for “cell morphology”
Supporting data for "Morphological profiling by high-throughput single-cell biophysical fractometry"
<p>No specific description. For more information, please contact: iriszqzh@connect.hku.hk.</p>
Unbiased single-cell morphology with self-supervised vision transformers -- Cell Painting
<p>The data necessary to reproduce the Cell Painting results in the paper <a href="https://www.biorxiv.org/content/10.1101/2023.06.16.545359v1">Unbiased single-cell morphology with self-supervised vision transformers</a>. </p>
Unbiased single-cell morphology with self-supervised vision transformers -- HPA FOV
<p>The data necessary to reproduce the HPA FOV results in the paper <a href="https://www.biorxiv.org/content/10.1101/2023.06.16.545359v1">Unbiased single-cell morphology with self-supervised vision transformers</a>. </p>
Unbiased single-cell morphology with self-supervised vision transformers -- HPA single cells
<p>The data necessary to reproduce the HPA single cells results in the paper <a href="https://www.biorxiv.org/content/10.1101/2023.06.16.545359v1">Unbiased single-cell morphology with self-supervised vision transformers</a>. </p>
Unbiased single-cell morphology with self-supervised vision transformers -- WTC11
<p>The data necessary to reproduce the WTC11 results in the paper <a href="https://www.biorxiv.org/content/10.1101/2023.06.16.545359v1">Unbiased single-cell morphology with self-supervised vision transformers</a>. </p> <p> </p>
Ovarian Morphology and Theca Cell Androgen Production in Women With Polycystic Ovary Syndrome (PCOS)
ClinicalTrials.gov study NCT02145247. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Data and code from: Imaging flow cytometry enables label-free cell sorting of morphological variants from populations of the unculturable bacterium <em>Pasteuria ramosa</em>
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Data from: Coordinated ARP2/3 and glycolytic activities regulate the morphological and functional fitness of human CD8+ T cells
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Data from: A data-driven approach to establishing cell motility patterns as predictors of macrophage subtypes and their relation to cell morphology
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Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts
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Dynamical forces drive cell and organ morphology changes during embryonic development
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Data for "A systematic evaluation of interneuron morphology representations for cell type discrimination"
<p>data_v1.1 contains all the data to reproduce the figures of the publication <em>A systematic evaluation of interneuron morphology representations for cell type discrimination (</em>https://doi.org/10.1101/591370<em>).</em></p> <p>statistic_descriptions.csv : links each feature's statistic_id with a short description</p> <p>classification: This folder holds the multi-class and the pairwise classification performances of all feature representations (relevant for figure 4 and figure 5). It also holds the pickled multi-class models trained on morphometric statistics which coefficients are visualized in figure S5.</p> <p>embedding_data: This folder holds all the data used for the t-SNE visualizations of figure 8 and S4.</p> <p>features: This folder holds all computed feature representations of each data set and each modality (full, axon, dendrite). Features are indexed by a statistic id. Some example features are shown in figure 2. Careful, this folder is large (~6GB)!</p> <p>reconstructions: This folder contains all the neural reconstructions used for figure 1.</p> <p>final morphologies: contains all pre-processed reconstructions used in this study.</p>
Data from: Morphological identification and single-cell genomics of marine diplonemids
Recent global surveys of marine biodiversity have revealed that a group of organisms known as "marine diplonemids" constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2 and 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids, isolated from a range of depths in the eastern North Pacific Ocean. Phylogenetic analysis confirms that the isolates reflect the entire range of marine diplonemid diversity, and comparisons to environmental SSU surveys show that sequences from the isolates range from rare to superabundant, including the single most common marine diplonemid known. SCG generated a total of ∼915 Mbp of assembled sequence across all ten cells and ∼4,000 protein-coding genes with homologs in the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed across categories expected for heterotrophic protists. Models of highly conserved genes indicate a high density of non-canonical introns, lacking conventional GT-AG splice sites. Mapping metagenomic datasets [4] to SCG assemblies reveals virtually no overlap, suggesting that nuclear genomic diversity is too great for representative SCG data to provide meaningful phylogenetic context to metagenomic datasets. This work provides an entry point to the future identification, isolation, and cultivation of these elusive yet ecologically important cells. The high density of nonconventional introns, however, also portends difficulty in generating accurate gene models and highlights the need for the establishment of stable cultures and transcriptomic analyses.
Wistar rat hippocampus CA1 pyramidal cell morphologies
<p>title : Reconstruction of hippocampus CA1 cell morphologies</p> <p>specimen : Rattus norvegicus</p> <p>sex : male</p> <p>strain : Wistar</p> <p>age : post-natal day 14-16</p> <p>This neuron was recorded and filled with biocytin (3 mg/ml) in a 300 µm thick coronal slice of rat hippocampus, using 2 - 10 MOhm patch pipettes. 3,3′-diaminobenzidine (DAB) was used for revelation. The slice was fixed and the cell reconstructed with Neurolucida using a 100x oil immersion objective.</p>
C57BL/6J mouse hippocampus CA1 pyramidal cell morphologies
<p>title : Reconstruction of hippocampus CA1 cell morphologies</p> <p>specimen : Mus musculus</p> <p>sex : male</p> <p>strain : C57BL/6J</p> <p>age : post-natal day 13-16</p> <p>This neuron was recorded and filled with biocytin (3 mg/ml) in a 300 µm thick coronal slice of rat hippocampus, using 2 - 10 MOhm patch pipettes. 3,3′-diaminobenzidine (DAB) was used for revelation. The slice was fixed and the cell reconstructed with Neurolucida using a 100x oil immersion objective.</p>
FIGURES 21–30 in Auxosporulation, morphology of vegetative cells and perizonium of Fallacia tenera (Hust.) D.G. Mann (Bacillariophyceae)
FIGURES 21–30: The fine structure of a complete cingulum. Bars in Figs 21, 22, 28 are 2 µm. Bars in Figs 23–27 and Fig. 28 are 1 µm. The bar in Fig. 30 is 500 nm. Fig. 21. A complete theca, two ligulae (arrow and arrowhead) of pleurae could been found at the two terminals. Fig. 22. An open valvocopula with undulate margin. Fig. 23. The internal view of a ligula (arrow) of the pleura 2 (the third band). Fig. 24. The external view of the ligula (arrow) of the pleura 2 (the third band). Fig. 25. The external view of a ligula of the pleura 1 (the second band). Fig. 26. The internal view of the ligula (arrowhead) of the pleura 1 (the second band). Fig. 27. The linear strip (arrow) of the pleura 2 (the third band). Fig. 28. The two terminals of the linear strips (arrows) of the pleura 2 (the third band). Fig. 29. The linear strip (arrow) of pleura 2 (the third band) and the linear strip (arrowhead) of pleura 1 (the second band). Fig. 30. The two terminals (arrowheads) of pleura 1 (the second band).
FIGURES 9–20 in Auxosporulation, morphology of vegetative cells and perizonium of Fallacia tenera (Hust.) D.G. Mann (Bacillariophyceae)
FIGURES 9–20: The fine structure of Fallacia tenera in SEM and TEM. All Scale bars = 1 µm except Figs 9, 10, 18 (2 µm) and Figs 19–20 (200 nm). Figs 9–10. Plan view (Figs 19–20) of external valve face and internal valve face. Figs 11–12. View of external and internal valve face at 30°tilt. Fig. 13. The detail of a frustule terminal. Note the finely porous conopeum (arrow) and two pores (arrowhead) lies beside the terminal fissures. Fig. 14. The broken valve shows a round areola (arrow) which should be covered by a conopeum and a "peg" (arrowhead), a silica flip. Fig. 15. The broken valve showing the depressed sterna (arrow). And also the "peg" (arrowhead) extend from the edge of the valve mantle. Fig. 16. The undulate margin of the conopeum. Fig. 17. The lumen between the conopeum and the valve (arrow), connecting outside through the terminal pores (arrowhead). Fig. 18. TEM photograph of a valve clearly shows the hyaline canal (arrowhead) and some silica structures (arrow) supporting the conopeum. Figs 19–20. The pattern of the areolae in longitudinal lines on the valve surface (fig. 19. Areolae are between the raphe and the canal, fig. 20, left) and on the mantle of valve. (fig. 20, right). They all belong to hexagonal array of hymen.
Supplementary material 8 from: Olszyński RM, Zakrzewski PK, Rimet F, Sulkowska J, Peszek Ł, Żelazna-Wieczorek J (2024) Morphology and phylogeny of Nitzschia nandorii sp. nov. (Bacillariophyceae), a new small-celled lanceolate species from a post-mining reservoir. PhytoKeys 241: 1-26. https://doi.org/10.3897/phytokeys.241.117406
Confocal Laser Scanning Microscopy projection of rotating chloroplast of Nitzschia nandorii sp. nov.
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Morphology of the studied Coelastrella strains. (4) IRK–A 2. (5) IRK–A 173. (А–D) vegetative cells and autosporangia. (E–G) cell wall ribs. (H) morphology of the old cells. Scale bar: 10μm.
FIGURE. Coprolites preserved in an early Permian fern mesophyll. A, Gross morphology of a fragmentary fern frond, specimen PB23532. B, Basal part of a penultimate pinna showing sphenopteroid vegetative pinnules. C, Polished surface showing two sporangia with typical annulus structures (white arrowheads). D, SEM image showing an in situ trilete spore. E, The fertile pinnule which contains numerous coprolites along a transverse wound area. F, Enlargement showing coprolites filled with brown to black contents. G, SEM image of the same part in E. H, SEM image showing locally preserved epidermal cells and nearby coprolites. in Discovery of coprolites in an Early Permian fern mesophyll
FIGURE. Coprolites preserved in an early Permian fern mesophyll. A, Gross morphology of a fragmentary fern frond, specimen PB23532. B, Basal part of a penultimate pinna showing sphenopteroid vegetative pinnules. C, Polished surface showing two sporangia with typical annulus structures (white arrowheads). D, SEM image showing an in situ trilete spore. E, The fertile pinnule which contains numerous coprolites along a transverse wound area. F, Enlargement showing coprolites filled with brown to black contents. G, SEM image of the same part in E. H, SEM image showing locally preserved epidermal cells and nearby coprolites.
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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.