cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03j3bqk
title: CIL:41368, Mus musculus, adenocarcinoma. In Cell Image Library

description: The image shows a slice through a 3D tomographic reconstruction of a mouse adenocarcinoma cell based on x-ray microscopy. Live cells were cryofixed by plunge freezing in liquid ethane and the vitrified material observed unstained using x-ray microscopy at a wavelength that yields high contrast between water and organic material. Images were taken over a range of specimen tilts from -60 to +60 degrees at 1 degree intervals. The image represents a 9.8 nm thick slice of the computed tomogram in the x-y plane, and shows the edge of the cell with filamentous cytoskeletal elements just below the plasma membrane. Cytoplasmic vesicles are also present. The black circular structure at bottom right is a bead used as a fiduciary marker. The images have a resolution of ~36 nm (Rayleigh Criterion) and ~70 nm (Fourier Ring Correlation), the latter corresponding to ~35 nm half-pitch resolution. Additional X-ray images from the study are included in this CIL Group. 
 See also: W G Muller et al. 2012 Towards an atlas of mammalian cell ultrastructure by soft X-ray tomography. J Struct Biol 177:179-192.
description: Preparation: cryofixed tissue
Relation to intact cell: slice of 3D tomogram
Item type: recorded image
Imaging mode: X-ray micrograph
Parameter imaged: x-ray scattering
Source of contrast: intrinsic mass distribution
Visualization methods: visualization of contiguous regions
Data qualification: Processed
description: Mouse adenocarcinoma cells were grown on gold grids coated with cellulose nitrate, incubated with 270 nm diameter gold-coated silica beads, plunge frozen in liquid ethane, transferred to a Gatan 630 cryoholder, and imaged at -170C in the frozen hydrated state using the X-ray microscope at the Helmholz Zentrum, Berlin, Germany. The microscope uses partially coherent illumination and a zone plate objective, and allows the specimen to be observed over a range of tilts. The images were aligned using the gold beads as fiduciary markers, and reconstructed using a reciprocal space algorithm. 
See: G Schneider et al. 2010 Three-dimensional cellular ultrastructure resolved by X-ray microscopy. Nat Meth 7:985-987.
DOI: 10.6075/j0pn94dn
title: CIL:40470, Homo sapiens, osteosarcoma. In Cell Image Library

description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody HPA022978 (shown in green). HPA022978 is a polyclonal anti-KRT24 antibody that labels intermediate filaments in these cells. Thee cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules (red).
description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal 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
description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met:

The publication and/or presentation are solely for informational and non-commercial purposes.

The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
DOI: 10.6075/j0gq6wp1
title: CIL:26599, Homo sapiens, cervical epithelium. In Cell Image Library

description: HeLa cells stably expressing the BAC-encoded GFP-labeled hPrp4 snRNP and MS2-mRED protein and treated with doxycholine to express the E3 transgene. Shown is the mRED signal. Cells imaged witb a Leica SP5 confocal microscope using a 60x 1.4NA HCX Plan Apo objective lens. From Fig 5C in Huranova et al. 2010 J Cell Biol 191:75-86.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; pDsRED-Monomer-N1
Processing history: line averaging
Data qualification: Processed
DOI: 10.6075/j0s75fvg
title: CIL: 52409, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=5, y=2, z=6 from BL024199_Myc_Terc
description: One z layer of a z-stack at the given tile position
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/j03777md
title: CIL:35534, Lilium longiflorum, gamete. In Cell Image Library

description: Lilium longiflorum (Easter Lily) pollen. This is a thin optical section through the center of the desiccated stage of the mature pollen showing autofluorescence or harmonic generation of intrinsic structures. The brightest signal is from the outer layer, the exine and raised pilae.
description: Preparation: unfixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: intrinsic mass distribution
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Illumination provided by a SpectraPhysics-Newport MaiTai laser with DeepSee dispersion compensation providing pulses of approximately 100 fs duration at 80 MHz. Wavelength set at 875 nm with emission at 465 to 50 nm.
Zeiss 710 multi-photon microscope with 63X N.A. 1.4 oil immersion objective. Pollen was removed from the flower, put in a coverslip bottom chamber, covered with tissue culture grade mineral oil, and imaged within 12 hours.
DOI: 10.6075/j06972wj
title: CIL:41610, Cricetulus griseus, epithelial cell, ovary. In Cell Image Library

description: CHO cells arrested at metaphase with colcemid were treated with 67% D2O, in 0.07M phosphate buffer and squashed in 50% acetic acid. Preparations were transferred to EM grids and examined with the Wisconsin HVEM operated at 1MeV.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: Preparation: chemically fixed tissue
Relation to intact cell: squash preparation
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High Voltage Transmission EM of whole mitotic metaphase chromosomes from Chinese hamster ovary cells. This image was recorded at a specimen tilt of 59 degrees and is grouped with one taken at 49 degrees, creating a stereo pair giving an oblique 3D view of the chromosomes.
DOI: 10.6075/j0qr4wcr
title: CIL:1058, Caenorhabditis elegans, muscle cell. In Cell Image Library

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
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 2 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.
DOI: 10.6075/j0hx1c27
title: CIL: 50878, Saccharomyces cerevisiae (baker's yeast, budding yeast), Old S. cerevisiae cells. In Cell Image Library

description: The cell surface of exponentially growing Saccharomyces cerevisiae cells was labeled with biotin by incubating the cells with 0,5 mg/ml Sulfo-NHS-LC biotin (#21335, Thermo Fisher scientific) for 20 minutes at room temperature. Cells were grown in YPD, harvested prior saturation of culture, and washed in PBS + 0,5% glucose. Biotinylated cells were labeled with 17.5 ug/ml Streptavidin magnetic beads (#21344, Thermo Fisher scientific) for 1.5 hours followed by 3 x 15 min magnetic sorting with PBS + 0,5% glucose washes in between. Another two rounds of growth, streptavidin-labeling, and sorting was performed. The old cells were recovered in YPD for 4 hours before high pressure freezing. Samples were high pressure frozen in a Wohlwend Compact 3 machine, followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead 
citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Old Saccharomyces cerevisiae cells were isolated with the use of Streptavidin magnetic beads. Then, isolated old cells were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
DOI: 10.6075/j0028r99
title: CIL: 54198. In Cell Image Library

description: TK 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/j05h7fc4
title: CIL:10705, Notophthalmus viridescens, oocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: High voltage TEM image of meiotic newt oocyte nuclei showing transcription on looped lampbrush chromosomes. This micrograph, was recorded at a tilt angle of 50 degrees. The image is grouped with one of the same sample area recorded at a 40 degree tilt. A stereo examination of the pair provides an oblique 3D view.
description: Oocytes were allowed to disperse in 30 mM KCl/NaCl, centrifuged through 2% formaldehyde onto an EM grid, stained with uranyl acetate, and critical point dried. Grids were examined with the Madison 1MeV TEM at 5 KX.
DOI: 10.6075/j03f4nvf
title: CIL:1637, Caenorhabditis elegans. In Cell Image Library

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
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 0 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.
DOI: 10.6075/j0mk6c4h
title: CIL:1636, Caenorhabditis elegans. In Cell Image Library

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
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 0 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.
DOI: 10.6075/j01835rk
title: CIL:1054, Caenorhabditis elegans, muscle cell. In Cell Image Library

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
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: 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 1 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.
DOI: 10.6075/j00864ws
title: CIL: 52712, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
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: Tile x=4, y=2, z=15 from PS11_10021_2B_Myc_Terc
DOI: 10.6075/j0qn65xz
title: CIL:16449, Prochloron. In Cell Image Library

description: Freeze-fracture replica of the unicellular photosynthetic prokaryote Prochloron showing the distribution and size of particles on cleaved thylakoid membranes. 
This image group includes many other freeze-fracture images of Prochloron.

See also: Giddings TH, Withers NW, Staehelin LA.1980 Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of Prochloron sp., a prokaryote. Proc Natl Acad Sci U S A. 77:352-3566.
description: Prochloron was collected at Coconut Island, Oahu, Hawaii. Green colonies of didemnid ascidians, Diplosoma virens, were collected from shallow waters. Green spherical cells, identified as Prochloron, were released from the ascidians by gently pressing on the colonies while flushing the surface with sea water. Cells were centrifuged, then rinsed in filtered sea water fixed with glutaraldehyde, infiltrated with glycerol and vitrified. Samples were fractured and replicated using a Balzers BA 360 freeze-etch device and examined and in a JEOL 100C TEM at 50,000X magnification. Images were recorded on film and digitized.
description: Preparation: freeze_fracture/freeze_etch; glutaraldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0v69htn
title: CIL:1644, Caenorhabditis elegans. In Cell Image Library

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
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: 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 0 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.
DOI: 10.6075/j06m35g0
title: CIL:38718, Chlamydomonas reinhardtii. In Cell Image Library

description: Isolated thylakoid membranes were cryoprotected with glycerol, cryofixed, fractured at -100C, shadowed with Pt, and replicas prepared by carbon coating. Cleaned replicas were examined with a Philips 300 TEM. See Goodenough and Staehelin 1971 J Cell Biol 48:595-619
description: Isolated chloroplast membranes of the unicellular photosynthetic alga Chlamydomonas reinhardtii were cryofixed, freeze-fractured, and surface replicas observed by transmission electron microscopy. These thylakoid membranes from the ac-31 mutant show the particle size and distribution typical of unstacked membranes. See Fig 21 in Goodenough and Staehelin 1971 J Cell Biol 48:595-619.
description: Preparation: cryofixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
DOI: 10.34740/kaggle/dsv/13565431
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.6075/j0v40t49
title: CIL:35386, Drosophila melanocephala, salivary gland. In Cell Image Library

description: Salivary glands were dissected, fixed with paraformaldehyde, post-fixed with osmium tetroxide, and embedded in plastic. 4 micron sections were cut, stained with aqueous uranyl magnesium acetate, and observed with the Wisconsin HVEM at 1 MeV. See Ris, H 1981 Stereoscopic Electron Microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris, H 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246
description: Preparation: chemically fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment; paraformaldehyde fixation
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: High Voltage (1MeV) TEM image of a 'thick' section of polytene chromosome from salivary gland of 3rd instar larva of Drosophila melanogaster showing the band-interband organization. This image was captured with a specimen tilt of 46 degrees. Grouped with it is an image of the same region taken at a tilt angle of 56 degrees, providing an oblique stereo view of the structure.
DOI: 10.6075/j02f7m87
title: CIL:39039, Termitidae, Trichonympha. In Cell Image Library

description: Photomicrograph of a semithin section of a termite's gut stained with haematoxylin and eosin. The gut appears to be packed with Trichonympha - a genus of protists found in the gut of many termite species. These symbiotic flagellates aid the termite in the digestion of cellulose in its food.
description: B0007739 Trichonympha in a section of termite gut. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: modes of light microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: hematoxylin; eosin
Processing history: unprocessed raw data