cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0sn0881
title: CIL:685, Zea mays, photosynthetic cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: raw unprocessed image
description: Zea mays seeds were germinated in the dark, briefly exposed to light, and segments of coleoptile, excised, fixed with glutataldehyde, post-fixed with osmuim tetroxide, and embedded in epoxy resin. Thin sections were cut, stained with uranyl acetate and lead citrate, and observed using a Philips 300 transmission EM. Images were recorded on film.
description: The plastids of plants germinated in the dark are termed etioplasts and possess quasi-crystalline structures termed prolammelar bodies that contain the phospholipid materials and chlorophyll precursors that are converted to green chloroplasts in response to light. The transmission electron micrograph shows a corn (Zea mays) etioplast fixed after brief exposure to light. The prolamellar body is still largely intact, but thylakoid membranes are starting to form and, in the lower portion, some stacking of thylakoids is seen.
DOI: 10.6075/j0xp73pk
title: CIL:12664, Danio rerio. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; osmium tetroxide 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: lead salt; uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Transmission EM showing adherens junctions between cells of the enveloping layer of a 24 hr (prim-5) Zebrafish embryo. Specimens fixed in Karnofsky's (overnight at 4˚C) followed by postfixing in 4% osmium tetroxide in .2M cacodylate for 1h. The resin was LX-112 and the stain was uranyl acetate and lead citrate. This image is part of a series taken by Bryan Crawford while he was at the University of Washington. They are part of the Zebrafish--The Living Laboratory CD made available by Mark Cooper and described in Methods in Cell Biology Volume 77, 2004, Pages 439-457.
DOI: 10.6075/j0v986ps
title: CIL:37911, Homo sapiens, epithelial cell. In Cell Image Library

description: Cultured monolayers were first treated with 30 µM SKI II (EMD) for 10 min. To induce apoptosis, monolayers were exposed to 1,200 µJ/cm2 UV254 irradiation in a UV series II (Spectroline) and incubated for 2 h before fixation. Cells were fixed with 4% formaldehyde in PBS, permeabilized with 0.5% Triton, blocked and incubated with primary antibody for 1 h (50 µg/ml anti-S1P mAb (LPath Inc.)). Secondary antibody was Alexa Fluor 488 goat anti–mouse IgG. Actin was detected with Alexa Fluor 568–phalloidin (Invitrogen). DNA was detected with 5 µM DRAQ5 (Axxora). Confocal micrographs were obtained using an inverted microscope (Eclipse TE300; Nikon) converted for spinning disc confocal microscopy (Andor Technologies) using a 60x Plan Fluor 0.95 oil lens with an electron-multiplied cooled CCD camera 1,000 x 1,000, 8 x 8 mm2 driven by the IQ software (Andor Technologies). ImageJ was used to stack confocal sections into Z series that were then color combined and reconstructed into 3D image using MetaMorph (GE Healthcare). All images were processed further using ImageJ, Photoshop (Adobe), Illustrator (Adobe), and Quicktime Pro (Quicktime) software. This Z-series corresponds to Fig 4D from J Cell Biol. 2011. 193(4): 667-676
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; phalloidin; DRAQ5
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Apoptotic cells produce and transmit the bioactive lipid sphingosine-1-phosphate (S1P) during extrusion. This set of images shows that extrusion is blocked, as well as accumulation of S1P around the dying cell, by SKI II, which blocks conversion of sphingosine to S1P. The apoptotic condensed nucleus is in blue, the actin-myosin ring at the basolateral surface is in red and S1P is in green.
DOI: 10.6075/j0610zkv
title: CIL:1122, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 4 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
DOI: 10.6075/j0mk6cg0
title: CIL: 52976, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Image 5, z=6 from SC_011
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
DOI: 10.6075/j0j67fmk
title: CIL:13407, Mus musculus, fibroblast. In Cell Image Library

description: Distribution of phosphorylated H2AX occurs preferentially in open chromatin. Wildtype mouse embryo fibroblasts were treated with the histone deacetylase inhibitor trichostatinA 8 hours before being incubated with the radiomimetic drug neocarzinostatin (NCS) for 1hour prior to being fixed and immunolabeled against the phosphorylated form of histone H2AX and co-stained with DAPI. MEFs were grown on glass coverslips and treated with 10 ng/ml NCS for 1 h or with 1 μM TSA for 8 h and were treated with 10 ng/ml NCS for an additional hour before being fixed in 2% freshly prepared PFA in PBS for 5 min at room temperature. Cells were immunolabeled using monoclonal antiphospho-H2AX antibody (clone JBW301; 1:1,000; Upstate Biotechnology) and goat anti–mouse AlexaFluor546 secondary antibody (Invitrogen). The cells were labeled for 30 min in PBS containing 100 nM DAPI, rinsed with PBS, and mounted on glass microscope slides in glycerol-based mounting media containing N-propyl gallate antifade (Sigma-Aldrich). A stack of confocal optical slices was captured through the depth of the nucleus (Z-axis) using a 63x Plan-Apochromat (N.A. 1.4) objective lens, an optical slice thickness of 800nm, a Z-step size of 200nm, and X-Y pixel size of 70nm. Individual optical slices were background subtracted and contrast adjusted only by stretching the histogram in a linear manner consistently for the different fluorescence channels.
Image corresponds to Fig 6B, right panel in Kim et al. J Cell Biol. 178: 209-218. 2007.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: single-spot confocal microscopy; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; differences in adsorption or binding of stain
Visualization methods: primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 546
Processing history: linear methods
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0mc8z9g
title: CIL:554, Acetabularia mediterranea, gamete. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: unprocessed raw data
description: Cysts were fixed in glutaraldehyde, post-fixed in osmium tetroxide, epoxy embedded, and thin sections stained with aqueous uranyl acetate and lead citrate. Grids were examined with a Philips 400 TEM operated at 80KV and images recorded on film.
description: At cyst formation in the 'giant' unicellular green alga Acetabularia, each cyst contains a single nucleus which subsequently undergoes several rounds of mitosis prior to gamete formation. Initially the nuclei form a syncytium which separates into individual gametes. This section shows a stage in gametogenesis where the syncytium has just started to divide into uninuclear gametes, and the formation of flagella from paired centrioles is in progress. See Woodcock and Miller, 1973. Ultrastructural features of the life cycle of Acetabularia I Gametogenesis. Proptoplasma 77, 313-319.
DOI: 10.6075/j0mc9041
title: CIL:40194, Rattus norvegicus, astrocyte of the hippocampus, astrocyte. In Cell Image Library

description: Male Sprague Dawley rats were anesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with either 5% aq. lucifer yellow. The astrocytes were filled using a 0.5 Hz pulses of
current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C, and subsequently immunostained. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000
(Hercules, CA) attached to a Nikon E600FN
(Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60× oil objective (NA 1.4). Optical z resolution is 0.25µm. Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injections of protoplasmic a 1-week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow (green) and immunostained to reveal the localization of glial-specific proteins S-100 (red) and GFAP (blue). Optical sections were generated with a single photon confocal microscope. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow; Alexa Fluor 568; X-Rhodamine; primary antibody plus labeled secondary antibody
Data qualification: Processed
DOI: 10.6075/j02n50w5
title: CIL:47657, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

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.
description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Vcam1)
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
DOI: 10.6075/j0bz65b1
title: CIL:2267, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 6 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: 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
DOI: 10.6075/j07d2t64
title: CIL:2838, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: 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
DOI: 10.6075/j07s7mw9
title: CIL:13127, 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution view of quick-freeze deep-etch of the contractile vacuole E-fracture face. This face, like the collecting canal membrane, is porous indicating that many IMPs have been removed from this leaflet during fracturing. The microtubular ribbon seen here is composed of at least 24 microtubules and is divided into 3 sub-ribbons. Only a few IMPs remain in this leaflet. TEM taken on 6/22/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 24,800X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0tq614m
title: CIL: 53075, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
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: Image 4, z=21 from SC_028
DOI: 10.6075/j0br8s7t
title: CIL:35913, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged TEM1. 
 
 TEM1 is a GTP-binding protein of the ras superfamily involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis. 
 
These phase,gfp images are part of an image group that ranges from CIL:35900-35919. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
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 electrons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
DOI: 10.6075/j0kw5fpx
title: CIL: 53381, Homo sapiens, HeLa. In Cell Image Library

description: CAMK 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.
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: Visualization methods: confocal microscopy
DOI: 10.6075/j00k28mf
title: CIL:36166, Rattus, multipolar neuron. In Cell Image Library

description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density of presynaptic contacts along the dendritic arbor.