cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0b857tv
title: CIL: 53813, 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: OTHER 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/j0z037gf
title: CIL:39524, Saccharomyces cerevisiae. In Cell Image Library

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 z-series images are part of an image group that ranges from CIL:39521-39525. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the 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.
DOI: 10.6075/j0vd6z40
title: CIL: 53992, 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: STE 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/j0m044dk
title: CIL:6516, Danio rerio, Eye. In Cell Image Library

description: This study of the zebrafish eye is a series of four images taken at increasing magnifications. This image, the first image is the SEM block face of the zebrafish eye. This is followed by a second image that is a higher magnification TEM image of the plexiform layer and the outer nuclear layer of the zebrafish retina. The third image is a 15,000X TEM image of the bipolar and horizontal cells interdigitating in the OPL layer of the zebrafish retina. The fourth image in the series is a higher magnification (60,000X) of the dense synaptic bar and synaptic vesicles.

This image of the larval zebrafish eye 10dpf was collected on a Gatan 3View® serial block face scanning electron microscope (SBFSEM). The 3View® is attached to a FEI Quanta 600 FEG SEM. Block face imaging is a way to look at epon embedded specimens using backscattered electrons in the SEM. A diamond knife in the vacuum chamber of the SEM cuts hundreds of ultrathin serial sections, thus gathering a perfected registered stack of images.

Reference for SBFSEM: Denk, W. and H. Horstmann. Serial block face scanning electron microscopy to reconstruct three- dimensional tissue nanostructure. PloS Biology vol 2, 11; e329 doi:10.1371/journal.pbio.0020329

Microwave processing, osmium tetroxoxide/osmid procedure for enhancing membranes, and copper lead en bloc staining.
Procedure for specimen preparation available at http://www.stanford.edu/~redhair/JoAnn_Buchanan.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; heat fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: tissue in epoxy resin embedment
Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; lead salt; copper salt
Processing history: unprocessed raw data
DOI: 10.6075/j0ff3r40
title: CIL:40485. In Cell Image Library

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.
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: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibodies (shown in green), the 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), (ii) anti-tubulin antibody as internal control and marker of microtubules, and (red), or (iii) calreticulin for the endoplasmic reticulum (ER) (yellow).
DOI: 10.6075/j0mw2fx7
title: CIL:50621, Homo sapiens, monocyte. In Cell Image Library

description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: One monocyte/polymorphonuclear-type cell contained several, partly lytic/aglutinated erythrocytes. There was a bifocal compression of the nucleus by erythrocytes.
description: Imaging mode: microscopy
Visualization methods: x100
DOI: 10.6075/j02b8wxd
title: CIL:35465, Rattus norvegicus. In Cell Image Library

description: Fenestrae of a Brown Rat arranged in sieve plates. Original magnification is 20,000x, a good indication of liver sinudosial endothelial cells (LESCs).
description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: scanning electron microscopy (SEM)
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: Raw;spatialmeasurements
description: Hitachi Field Emission SEM model S-4700.
DOI: 10.15468/dl.cvnsas
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Eleocharis uniglumis"
 ]
}

 The dataset includes 31 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009602-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0z036th
title: CIL:39083, Triticum sp., leaf. In Cell Image Library

description: Thylakoid preparations were equilibrated with 35% glycerol, plunge frozen in liquid Freon 12 cooled in liquid N2 and fractured and replicated in a Balzers BA 360 freeze etch device. Replicas were examined in a JEOL 100C at 80KV and images recorded on film. See Fig 9 in K D Allen et al. 1988 Biogenesis of thylakoid membranes is controlled by light intensity in the conditional chlorophyll b-deficient CD3 mutant of wheat. J Cell Biol 107:907-919.
description: CD3 mutant wheat (deficient in chlorophyll b) was germinated and grown for 6 days in the dark, greened at high light intensity, thylakoids prepared, plunge-frozen, and freeze-fracture replicas obtained and examined by transmission electron microscopy. This region shows the characteristic particle size and distribution found on the stacked (EFs, PFs) unstacked (EFu, PFu) membrane faces of stacked thylakoid membranes. Compared to the wildtype, there is increased density of particles on the EFs and EFu faces and decreased density on the PFs faces. This set of grouped images, which also shows thin sections, includes images of wild-type wheat.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
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: Processed
DOI: 10.6075/j0dj5fpx
title: CIL:32111, Homo sapiens, osteocarcenoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
DOI: 10.6075/j0z31xvx
title: CIL:13115, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution view of the Contractile Vacuole Complex. The CV membrane has collapsed into regularly spaced tubules oriented perpendicular to the microtubular ribbon in this ruptured cell. Some tubules and some nearby vesicles contain electron opaque material probably obtained from the mixture of the external medium and cytosolic contents as the CV expelled its content and medium had a chance to enter the CV by backflow. TEM taken on 8/8/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0tb1623
title: CIL:13111, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Cross section through a radial arm of the contractile vacuole complex. The collecting canal occupies the center of the arm whose membrane is supported by the radial microtubular ribbon which has now divided into at least six segments and surrounds the canal. Gaps between the segments are where the mass of membrane tubules of the smooth spongiome opens into the canal. Decorated tubules occurring in bundles form the peripheral layer of the radial arm. TEM taken on 5/2/79 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 18,000X. Bar = 0.2µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:13105) is in the library and available for quantitative analysis. 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/).
DOI: 10.6075/j0b27td6
title: CIL:13110, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Radial arm of the contractile vacuole complex displaying two rows of openings from the smooth spongiome into the collecting canal. Two microtubules separate the two rows of openings. The smooth spongiome forms a thick coat of membrane tubules around the canal and outside this is a reduced number of decorated spongiome tubules. TEM taken on 2/28/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,250X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:13101) is in the library and available for quantitative analysis. 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; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j03t9gcs
title: CIL:13107, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: A part of the CVC complex with some filled ampullae present. Masses of collapsed CV membrane are associated with the 11 microtubular ribbons. Ribbon 9 is curving away from the other ribbons and is extending out over an ampulla where it will continue along the full length of this radial arm. TEM taken on 3/27/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,250X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12995) is in the library and available for quantitative analysis. 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/).
DOI: 10.6075/j07s7n02
title: CIL:1313, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the dividing macronucleus shows it may be porous to microtubules. Segments of microtubules are found both outside and inside the nuclear envelope in this figure although one cannot follow a single microtubule through the nuclear envelope. The section is immunogold labeled with anti-b-tubulin. TEM taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0fb522j
title: CIL:13132, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: In defecation, when a spent vacuole has fused with the single membrane along the midline of the ridge the lips of the cytoproct split apart and form a wide gap. The membrane of the spent vacuole is now continuous with the plasma membrane and quickly undergoes vesiculation into vesicles that are released back into the cytosol. No membrane is released into the surrounding environment. The cytoproct lips are covered by extensions of alveoli up to their tips. Complete defecation is insured by the retrieval of all of the spent vacuole membrane until the lips are pulled back together at the tip of the ridge and all DV-IV membrane has been removed from the cytoproct. No other expulsion force is needed for expelling the vacuole contents. TEM taken on 5/25/82 by R. Allen with Hitachi HU11A operating at 60kV. Neg. 6,500X. Bar = 1µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:38701) is in the library and available for quantitative analysis. 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/).