cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0x92946
title: CIL:11486, Rattus, hepatocyte. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
description: Figures 282 (upper) and 283 (lower) from Chapter 9 (Peroxisomes) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Examples longitudinal, or transverse sections through peroxisomes from rat liver hepatocytes reveal the lattice of the urate oxidase crystal contained within the peroxisome. Upper image by Daniel Friend; lower panel by Richard Wood. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j06h4g6g
title: CIL:11626, Rattus sp., tracheal epithelial cell. In Cell Image Library

description: A figure from Chapter 13 (Cilia and Flagella) of 'The Cell' by Don W. Fawcett M.D. The microtubules of the axoneme are adequately preserved by routine fixation for electron microscopy of thin sections. These methods are less satisfactory for their subunits and appendages and have contributed little to our understanding of the organization of the ciliary matrix. Addition of tannic acid to the fixative results in an apparent thickening and a more intense staining of these components. The dynein arms are made more conspicuous, the radial spokes more robust, and the unstained protofilaments in the wall of the microtubules are clearly revealed in negative image. A copy of the chapter is available on the ASCB's BioEDUCATE website.
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; tannic acid
Processing history: recorded image; film; Scanned print from negative
Data qualification: Processed
DOI: 10.15468/dl.dexs2h
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Anaphalis nepalensis"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009236-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zad983
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Thylacospermum caespitosum"
 ]
}

 The dataset includes 29 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009237-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6353q6
title: Occurrence Download

description: A dataset containing 1153716 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (Plantas vasculares)"
 ]
}

 The dataset includes 1153716 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009224-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0s75f1q
title: CIL:15794, Dendraster excentricus. In Cell Image Library

description: Single-plane sequences of anucleate, centrosome-containing cytoplasts (sand dollars) expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). This anucleate cytoplast has four centrosomes, two in focus. In normal cells this size, furrowing would begin between 03:00 and 07:00, but no furrow occurs even 20 min later. Centrosomes are closer than the distance to the equator. Embryos were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C. Video corresponds to the first segment of video 6 and Fig 7A in J Cell Biol. 2009 Dec 14;187(6):831-45.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0cv4g9t
title: CIL:47555, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Mac1)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
DOI: 10.6075/j02v2dzz
title: CIL:10840, Phodopus, hepatocyte. In Cell Image Library

description: Figures 264 (upper) and 265 (lower) from Chapter 8 (Lysosomes) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Lysosomes apparent in thin sections from liver tissue of hamster treated with phenobarbitol. Primary lysosomes have dense homogeneous content, but the majority of the membrane-bounded dense bodies in the accompanying figures are secondary lysosomes. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
DOI: 10.6075/j0639nff
title: CIL:13476, Drosophila melanogaster, garland cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: fluorescence microscopy; confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: EGFP; Cy3
Data qualification: Raw
description: Ema localizes to endosomes. Third instar larval garland cells expressing Ema-GFP fusion protein with endosomes labeled with a 5-min pulse of the fluid-phase endocytic tracer avidin-Cy3 followed by an additional 5-min chase. Ema localizes to functional endosomes. Third instar larvae were dissected in ice-cold PBS, equilibrated in the Schneider medium for 5 min at room temperature, pulsed with 10 µg/ml of Extravidin-Cy3 (Sigma-Aldrich) at room temperature for 5 min, rinsed thoroughly, and chased in Schneider medium. Samples were fixed in 4% PFA in PBS for 10 min at room temperature. Confocal images were acquired with a confocal microscope (model C1; Nikon) and accompanying EZ-C1 software using argon (excitation at 488 nm) and HeNe (excitation at 543 and 633 nm) lasers and a 60x Plan-Apochromat NA 1.4 objective (Nikon) at room temperature. Samples for each experiment were processed using the same confocal gain setting. Image corresponds to Fig 3A in Kim et al. J Cell Biol. 188: 717-734. 2010.
DOI: 10.6075/j07p8z21
title: CIL: 53774, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: CMGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.6075/j0vh5nzp
title: CIL:39660, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0b27twg
title: CIL: 53218, Entire Organism, Overall development. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: Captured on a microscope using a Canon Rebel Ti5/6 or a one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of African clawed frog embryonic development. Each video is labeled with the temperature (Celcius) at which it was captured and the name of the Time Course (##TC).
DOI: 10.6075/j0125rk2
title: CIL:25514, Drosophila melanogaster, salivary gland. In Cell Image Library

description: Salivary glands from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film, are transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV.
description: Whole mount squash of polytene chromosome from Drosophila salivary gland. Image showing a series of bands and interbands was taken with a High Voltage EM at a tilt angle of 45 degrees. The accompanying grouped image, taken at 55 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j04m93h8
title: CIL:35653, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc20, a cell-cycle regulated activator of anaphase-promoting complex/cyclosome (APC/C) required for metaphase/anaphase transition; directs ubiquitination of mitotic cyclins, Pds1p, and other anaphase inhibitors; potential Cdc28p substrate novel protein thought to be involved in cell cycle regulation.These phase,gfp images are part of an image group that ranges from CIL:35640-35659. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.15468/dl.xw7p4d
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Salsola nitraria"
 ]
}

 The dataset includes 63 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009238-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0rx9bhv
title: CIL: 51666, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j0b856rj
title: CIL:37189, Rattus, hepatocyte. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x18,000.
description: Transmission electron micrograph of rat liver showing rough endoplasmic reticulum, mitochondria, and glycogen granule rosettes. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0m04406
title: CIL:49952, Primary human small airway epithelial cells immortalized with telomerase. In Cell Image Library

description: Primary human small airway epithelial cells in interphase state were fixed with 2.5% glutaraldehyde, 5 mM CaCl<sub>2</sub> in 0.1 M sodium cacodylate buffer (pH 7.4). Cells were stained with 10 µM DRAQ5, and photo-oxidized at 620 ± 30 nm for 8 minutes. Cells were post-fixed with 2% osmium tetroxide, 2 mM CaCl<sub>2</sub>, 1.5% potassium ferrocyanide in 0.15 M sodium cacodylate buffer (pH 7.4). Samples were ethanol dehydrated, embedded in Durcupan epoxy resin and sectioned to 250 nm thickness and mounted on copper slot grid. 5 nm and 10 nm colloidal gold particles were deposited on the grid as fiducial markers. 8-tilt EM tomography was collected on a 300 kV FEI Titan Krios using a 4K by 4K Gatan Ultrascan CCD camera at 1 degree increment for each tilt series from -60° to +60°. The entire set of EMT images was aligned and reconstructed using the Transform-based Tracking, Bundle adjustment, and Reconstruction (TXBR) package. The data has a voxel size of 2.04 nm.
description: Multi-tilt EM tomogram of primary human small airway epithelial cell (SAEC) in interphase state. The tomogram refers to the SAEC in figure S8 of the published manuscript: 
http://science.sciencemag.org/content/357/6349/eaag0025
description: Preparation: Glutaraldehyde fixed cells, photo-oxidation of DRAQ5 in the presence of DAB solution to induce DAB polymerization and subsequent staining with osmium tetroxide
Relation to intact cell: semi-thin section ~250 nm
Item type: recorded image
Imaging mode: 8-tilt EM tomography
Parameter imaged: electron density
Source of contrast: Osmium tetroxide staining of DAB polymers catalyzed by photo-oxidation of DRAQ5 stained cells in the presence of DAB solution
DOI: 10.6075/j0dn44nd
title: CIL: 53057, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 4, z=3 from SC_028
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0bg2mvs
title: CIL:39736. In Cell Image Library

description: Reconstituted chromatin was fixed with 0.1% glutaraldehyde for 30 min, deposited on glow discharged carbon films, negatively stained with aqueous uranyl acetate, and examined with a FEI Tecnai F30 TEM operated at 200 KV.
See also: Routh et al. (2008) Nucleosome repeat length and linker histonen stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105:8872-8877.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image; portrayed image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: negative staining; uranyl salt
Processing history: montage
Data qualification: Processed
description: Images of negatively stained chromatin fibers prepared from tandem arrays of a nucleosome positioning sequence reconstituted with purified histones together with the results of Monte Carlo simulations of chromatin folding. Top left - 167 bp repeat with no linker histone; upper right - 197 bp with without linker histone; lower left 167 bp with linker histone H5; lower right 197 bp with linker histone. .
 See: Fig 4 in Routh et al. (2008) Nucleosome repeat length and linker histonen stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105:8872-8877.
DOI: 10.6075/j0dr2tbx
title: CIL:41563, Penium margaritaceum. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: autofluorescence
description: Confocal micrograph of a green alga, Penium margaritaceum. The cell wall is shown in green and the chloroplast is represented by autofluorescence.
 Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j0b8571j
title: CIL:36627, 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; Print of negative scanned for Photoshop
Data qualification: Processed
description: The cytoplasm of P. multimicronucleatum like all other cells contains a large number of organelles that are membrane bound. Membranes are used to compartmentalize and isolate metabolic and enzymatic processes within a continuous cytosol and cytomatrix which is the background phase of the cytoplasm. The principle site of biogenesis for secretory proteins, lysosomal hydrolases and membrane lipids and proteins is the endoplasmic reticulum, a system of membrane cisternae and tubules. This quick-freeze deep-etch preparation of a living cell shows an extensive fracture through the ER showing its P-fracture face. Intramembrane particles (IMPs) form clumps and patterns rather than being evenly spread within the membrane. Some of these IMPs probably represent sites of ribosome attachment to translocons. Translocons are intramembrane pores through which proteins are translocated into the ER during their translation. The flattened ER cisternae morph into tubular ER. TEM taken on 6/5/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.2µm.