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Text-fig. 24. Scanning electron microscope (SEM) images (a, c, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images (b, e) of fruits and seeds of Serialis antiqua (a, b) and Serialis parva (c–e); Torres Vedras locality, Portugal. a, b) Serialis antiqua lateral view of fruit showing smooth partly abraded fruit wall (a) and longitudinal section (b, SRXTM orthoslice yz0862) showing six closely adhering seeds, some of which are mature with well-preserved nutritive tissue; c–e) Serialis parva lateral view of fruit showing faint ribs (c), finely pitted seed surface with undulate anticlinal walls of the exotestal cells (d), and transverse section showing two closely adhering seeds (SRXTM orthoslice xy0913, e). Specimens, TV43-S174480 (a, b), TV43-S170076 (c), TV43-S170079 (d), TV43-S174477 (e). Scale bars 300 Μm (a–c, e), 50 Μm (d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 24. Scanning electron microscope (SEM) images (a, c, d) and synchrotron radiation X-ray tomographic microscopy (SRXTM) images (b, e) of fruits and seeds of Serialis antiqua (a, b) and Serialis parva (c–e); Torres Vedras locality, Portugal. a, b) Serialis antiqua lateral view of fruit showing smooth partly abraded fruit wall (a) and longitudinal section (b, SRXTM orthoslice yz0862) showing six closely adhering seeds, some of which are mature with well-preserved nutritive tissue; c–e) Serialis parva lateral view of fruit showing faint ribs (c), finely pitted seed surface with undulate anticlinal walls of the exotestal cells (d), and transverse section showing two closely adhering seeds (SRXTM orthoslice xy0913, e). Specimens, TV43-S174480 (a, b), TV43-S170076 (c), TV43-S170079 (d), TV43-S174477 (e). Scale bars 300 Μm (a–c, e), 50 Μm (d).
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f).
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f).
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 22. Scanning electron microscope (SEM, a–c) and synchrotron radiation X-ray tomographic microscopy (SRXTM, d) images of Ibericarpus cuneiformis gen. et sp. nov.; Catefica locality, Portugal. a) Fruiting axis bearing an elongated receptacle with numerous diamond-shaped scars from detached fruitlets; note the absence of scars from bracts, tepals or stamens at the transition to the fruitlet scars and the stalk (arrow); b) Group of ten fruitlets detached from fruiting axis in (a) showing apical stigmatic region and distinctive bulging isodiametric epidermal cells; c) Detached fruitlet showing apical stigmatic region; d) Volume rendering of three adhering fruits showing apical stigmatic region and distinctive bulging isodiametric epidermal cells. Specimens, Catefica MM75-P0477 (a, b), Catefica 49-S115852 (c), Catefica 50-S174907 (d). Scale bars = 300 Μm (a–d).
Data from: Automated workflow for the cell cycle analysis of (non-)adherent cells using a machine learning approach
Open the record for dataset details and reuse information.
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 10
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 10 comprises an image series of 255 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 05
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 05 comprises an image series of 500 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 6 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 03
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 03 comprises an image 3D model of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. The model was generated by segmentation of the entire cell, the cell nuclei (red) and the ventral disc cytoskeleton (yellow) in an image series of 276 images which was recorded by SBF SEM (see dataset 01). Section interval was 50 nm and pixel size 10 nm. The data folder contains the model-file (Imaris-format) and a 360° rotation of the model as video file (mp4-format).</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 02
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 02 comprises an image series of 1462 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 5 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 09
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 09 comprises an image series of 400 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 08
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 08 comprises an image series of 299 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 3 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 04
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 04 comprises an image series of 120 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 07
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises an image series of 318 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 8 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 06
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 06 comprises an image series of 215 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 01
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 comprises an image series of 276 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 4 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Growth kinetics of the HSJD-DIPG-07 cell line in non-adherent culture
<p>The growth kinetics of the HSJD-DIPG-07 cell line when grown as neurospheres in non-adherent culture conditions.</p>
Annotated quantitative phase microscopy cell dataset of various adherent cell lines for segmentation purposes
<p>This dataset contains microscopic images of multiple cell lines captured by quantitative phase microscopy (QPI) without use of any fluorescent labeling and a manually annotated ground truth for subsequent use in segmentation algorithms. Dataset also includes images reconstructed according to the methods described below in order to ease further segmentation. </p> <p>Our data consist of quantitative phase microscopy images:</p> <ul> <li>244 labelled images of PC-3 (7,907 cells), 205 labelled PNT1A (9,288 cells), 25 labelled images of G361, 25 labelled images of A2050 and 25 labelled images of HOB cells , in the paper designated as "<em>labelled"</em>, and</li> <li>1,819 unlabelled images with a mixture of 22Rv1, A2058, A2780, DU145, Fadu, G361, HOB and LNCaP used for pretraining, in the paper designated as "<em>unlabelled"</em>.</li> </ul> <ul> <li>See Vicar et al. XXXX 2021 DOI XXX (TBA after publishing)</li> <li>Code using this dataset is available at <a href="https://github.com/tomasvicar/Deep-QPI-Cell-Segmentation">github.com/tomasvicar/Deep-QPI-Cell-Segmentation</a></li> </ul> <p><strong>Materials and methods </strong></p> <p>A set of adherent cell lines of various origins, tumorigenic potential, and morphology were used in this paper (PC-3, PNT1A, 22Rv1, DU145, LNCaP, A2058, A2780, Fadu, G361, HOB). PC-3, PNT1A, 22Rv1, DU145, LNCaP, A2780, and G361 cell lines were cultured in RPMI-1640 medium, A2058, FaDu, and HOB cell lines were cultured in DMEM-F12 medium, all supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml), and with 10% fetal bovine serum (FBS). Prior to microscopy acquisition, the cells were maintained at 37 °C in a humidified (60%) incubator with 5% CO\textsubscript{2} (Sanyo, Japan). For acquisition purposes, the cells were cultivated in the Flow chamber µ-Slide I Luer Family (Ibidi, Martinsried, Germany). To maintain standard cultivation conditions during time-lapse experiments, cells were placed in the gas chamber H201 - for Mad City Labs Z100/Z500 piezo Z-stage (Okolab, Ottaviano NA, Italy). For the acquisition of QPI, a coherence-controlled holographic microscope (Telight, Q-Phase) was used. Objective Nikon Plan 10×/0.3 was used for hologram acquisition with a CCD camera (XIMEA MR4021MC). Holographic data were numerically reconstructed with the Fourier transform method (described in Slaby, 2013 and phase unwrapping was used on the phase image. QPI datasets used in this paper were acquired during various experimental setups and treatments. In most cases, experiments were conducted with the time-lapse acquisition. The final dataset contains images acquired at least three hours apart.</p> <p><strong>Folder structure and file and filename description</strong></p> <p><strong>labelled </strong><em>(labelled)</em>: cells with segmentation labels, e.g.<br> 00001_PC3_img.tif - 32bit tiff image (in pg/um2 values)<br> 00001_PC3_mask.png - 8bit image with mask with unique grayscale value corresponding to single cell in FOV.</p> <p><strong>unlabelled </strong><em>(unlabelled)</em>: 11 varying cell lines, total 1819 FOVs, 32bit tiff image (in pg/um2 values)</p> <p> </p>
Adherence Interventions for HIV Youth Via Text & Cell Phone - Sequential Multiple Assignment Randomized Trial (SMART)
ClinicalTrials.gov study NCT03535337. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cell Phone Support to Promote Medication Adherence Among Adolescents and Young Adults With Chronic Illness
ClinicalTrials.gov study NCT04241627. IPD Sharing: NO. Countries: 1. Publications: 3.
Hydroxyurea Adherence for Personal Best in Sickle Cell Disease (HABIT): Efficacy Trial
ClinicalTrials.gov study NCT03462511. IPD Sharing: NO. Countries: 1. Publications: 6.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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
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