cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0x63m82
title: CIL:40555, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibodies
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density; intrinsic mass distribution
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; gold; uranyl salt
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: To label membranes inside the cell we used very lightly fixed cells (0.25% glutaraldehyde) that were then rapidly frozen in liquid nitrogen and sectioned later at -100oC. These frozen sections were picked up on drops of methylcellulose and transferred to a Formvar-supported grid. The sections were immunogold labeled (15nm gold) to show the location of the specific antigen inside the cell as well as on the cell surface. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Immunogold label specific for Q2 antigen on discoidal vesicles. The same mAb used in CIL:36721 heavily labels discoidal vesicles and less heavily the cytopharyngeal membrane. A few gold particles are also found on the acidosomes. The distribution of this label confirms that the discoidal vesicles fuse with the cytopharynx to form the phagosome. TEM taken on 10/24/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X.
DOI: 10.6075/j0vt1qvr
title: CIL:40553, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
description: The nascent phagosome membrane has a dense coat of acidosomes docked at its cytosolic surface well before the nascent vacuole pinches off the cytopharynx. This micrograph is a quick-freeze deep-etch image of a transverse section through the posterior portion of the buccal cavity with a nascent vacuole bulging from the cytopharynx. Living cells were spun down in a centrifuge and a slurry of cells was mounted on a copper support before slam freezing the living cells against a highly polished copper surface. Some paramecia had been disrupted and this cell was feeding on the particulate organelles of the disrupted cells. Thus the nascent vacuole contains these particles amassed against its luminal surface. The cilia in the buccal cavity obviously efficiently sweep the particles against the dorsal posterior surface. TEM taken on 5/26/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 4,000X. Bar = 1µm. Published in J. Cell Sci. 106:411-422, 1993. Adapted with permission.
description: The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0610z6x
title: CIL:40505, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High magnification view of a crushed mitochondrion showing the zipper-like row of 9nm diameter particles on the outer curve of the cristae and the single row of larger particles on the inner curve. There is an average of 1500 particles per square micrometer of 50-nm tubular cristae surface on the outer curve. These particles are thought to be the F1 units of the F1F0 ATP synthases of the mitochondria. The larger particles on the inner curve resemble complex I of the respiratory electron transport chain in size and relative abundance when compared to their relative quantities estimated from biochemical studies in other cells such as beef heart. This shows the highly ordered arrangement of some of the molecules of the oxidative phosphorylation and electron transport systems in Paramecium. TEM taken on 5/6//88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 63,000X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/). Published in J. Cell Biol. 108:2233-2240, 1989. Adapted with permission.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0rr1x1v
title: CIL:40662, Rattus, hippocampal neuron. In Cell Image Library

description: Platinum replica depicting the cytoskeletal organization of dendritic spines in extracted 14 DIV neurons. Branched actin filaments (cyan) in the head. Image corresponds to Figure 2a in Mol Biol Cell. 2010 Jan 1;21(1):165-76. The entire panel is available as CIL 40660. The uncolorized image is available as CIL 40659. Box 1, 2 (this image), and 3 are CIL 40661, 40662, and 40663, respectively.
description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: grey scale graphic
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: colorized
DOI: 10.6075/j0gq6wnk
title: CIL:40659, Rattus, hippocampal neuron. In Cell Image Library

description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
description: Platinum replica depicting the cytoskeletal organization of dendritic spines in extracted 14 DIV neurons. Mushroom spines associate with dendrites at the base (bottom) and with axons by the head (top). Thick fibers in neurites represent microtubules. Image corresponds to Figure 2a in Mol Biol Cell. 2010 Jan 1;21(1):165-76. The entire panel is available as CIL 40660. The uncolorized image (this image) is available as CIL 40659. Box 1, 2, and 3 are CIL 40661, 40662, and 40663, respectively.
description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: grey scale graphic
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0j102h9
title: CIL:40628, Gallus gallus, cochlear inner hair cell. In Cell Image Library

description: Chicken basilar papilla (cochlea) hair bundles imaged with field-emission scanning electron microscope.
description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j06h4gq6
title: CIL:40573, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: The 11 micrographs of the group are views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows 1 food vacuole; a segment of the macronucleus; the micronucleus; the contractile vacuole, linked by CV pore to the bacteria-filled chamber; peristome; perioral cilia now closed to the outside. A sand grain (shattered during sectioning) was trapped against the cell by an unknown layer of unstained material. TEM taken on 3/17/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,000X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0sf2twd
title: CIL:12212, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Metaphase in INCENP-OFF cells expressing TrAP-INCENP F802A. Histone H3 modification H3-T3ph shown in red and H3-S28ph in green. DAPI (DNA) is blue. See Supplementary Fig 3G panels 8-11 in Supplementary data for Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.15468/dl.8tuqyb
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Oryza sativa"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009599-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0sq8z47
title: CIL:12208, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Prometaphase localization of INCENP (red) in INCENP-OFF cells expressing TrAP-INCENP F802A. Endogenous Aurora B is green and DAPI (DNA) is blue. See Supplementary Fig 3C panels 1-4 in Supplementary data for Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j02f7m4f
title: CIL:12218, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Anaphase in INCENP-OFF cells expressing TrAP-INCENP WT. Histone H3 modification H3-S20ph shown in green. DAPI (DNA) is blue. See Supplementary Fig 3E panels 12-14 in Supplementary data for Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0cf9nz5
title: CIL:41637, Rattus, astrocyte. In Cell Image Library

description: Confocal micrograph of a rat cerebral cortex with astrocytes‚Äô (yellow) endfeet wrapping around blood vessels (red). Cell nuclei are cyan. The image was collected using spectral imaging with 50 Z-slices. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
description: Item type: recorded image
Imaging mode: confocal microscopy; spectral imaging
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Processing history: z projection
DOI: 10.6075/j09g5m63
title: CIL:44505, Canis lupus familiaris, kidney epithelial cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Time series light microscopy images illustrating a wound healing assay. A monolayer of MDCK (Madin-Darby Canine Kidney) epithelial cells is scratched to create a 'wound' about 300 micrometers in width, after which the growth of the cells to fill the wound is monitored by recording images over the course of 15h.This image is part of a group of 12 that includes control cells (CIL:44501, 502, 506, 507, 508) and after addition of Hepatocyte Growth Factor /Scatter Factor (HGF/SF) to activate HGF/SF-Met signaling (CIL:44503, 504, 505, 509, 510). Also in the group are two movies, one control (CIL:44511), and one HGF/SF treated (CIL:44512). For additional wound healing assays see CIL:43401 and images grouped with it.
description: Madin-Darby Canine Kidney (MDCK) epithelial cells expressing YFP-membrane were maintained in DMEM supplemented with 5% fetal FCS in a 37°C, 5% CO2 incubator.
Wound healing assay: Cells were grown to 90% confluence in 24-well plates. Prior to scratching, the cells were starved by changing the medium to DMEM plus 0.1% FCS (starvation medium) for 24 hours. The medium was then changed to either fresh starvation medium (control), or starvation medium with 80 ng ml-1 HGF/SF for an additional 2 hours. A scratch of approximately 300 μm in width was generated using a 200 μl tip. The plate was subjected to time lapse microscopy in a stage incubator (OKOLAB, Italy) on a computer-controlled motorized stage of a confocal microscope (CLSM-510, Carl Zeiss, Germany), used in non-confocal DIC mode, with a 10x (NA 0.30) objective. Image acquisition was initiated 2 hours post scratching. Images were acquired every 15.7 minutes for 15 hours. The coordinates of each scratch were predefined, and a macro that repetitively positions the field of view at each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence was used for the analysis.
DOI: 10.6075/j04t6h3s
title: CIL:13455, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-GOLPH3 in BY4742 vps74∆. GFP-GOLPH3 is localized to Golgi compartments and the cytosol. Control image for images showing ectopic expression of GFP-GOLPH3 with mutations in the sulfate-binding pocket (CIL#s 13456, 13457). This study demonstrates that the sulfate-binding pocket of Vps74 and GOLPH3 mediates PtdIns4P-binding and is essential for function. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4A GFP-GOLPH3 wild-type/vps74∆ panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4A include CIL#s 13449, 13451, 13453, 13455, 13456, 13457, 24816, 24817, 24818, 24819, 24820, 24821.
DOI: 10.6075/j03r0s48
title: CIL:222, mast cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: secondary electron generation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
description: A scanning electron microscope image of an activated mast cell illustrating the convoluted topography of the cell membrane, which is populated with receptors.
DOI: 10.6075/j01n7zt9
title: CIL:13471, Drosophila melanogaster, garland cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Data qualification: Raw;intensitiesquantitation
description: Transmission electron micrograph of Drosophila nephrocyte garland cell. Wild-type garland cells display extensive tubulo-vesicular and vacuolar profiles of endosomal compartments, including electron-lucent alpha vacuoles akin to early endosomes in the cell cortex, and electron-dense beta vacuoles that represent late endosomes more centrally. The largest vacuoles in wild type are 2 microns in diameter and all vacuoles contain a single aggregate of electron-dense granular material that appears to be attached to the limiting membrane. Samples for TEM were fixed for 1 h at 4°C in 2% paraformaldehyde, 2% glutaraldehyde, and 1% tannic acid in 0.1 M cacodylic acid buffer, pH 7.2. Then, the samples were postfixed in 1% OsO4 in 0.1 M cacodylic acid buffer, pH 7.2, for 1 h at room temperature, stained en bloc with 1% uranyl acetate, dehydrated in a grade series of ethanol and propylene oxide, and embedded in epon resin (Electron Microscopy Sciences). Blocks were sectioned in an ultramicrotome (RMC Products) at ∼70-nm thickness with a Delaware Diamond knife and post-stained for 1 h in Reynolds lead citrate and uranyl acetate. Electron micrographs were taken on a transmission electron microscope (H-7500; Hitachi) using an AMT camera system. Mag: 15000x. Image corresponds to Figure 2C, left WT panel in Kim et al. J Cell Biol. 188: 717-734. 2010. This is a high magnification view of the region in CIL# 13470.
DOI: 10.6075/j0hq3xn5
title: CIL:13467, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis (the Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1) ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the isogenic control strain for the frq1-1 mutant at permissive temperature of 26C. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4D 26C FRQ1 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation