cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03x868s
title: CIL: 53376. 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: 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.
DOI: 10.6075/j0v12490
title: CIL: 52421, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=5, y=2, z=18 from BL024199_Myc_Terc
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 tile position
DOI: 10.6075/j0vm4btt
title: CIL: 52892, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 9, z=6 from SC_007
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/j02r3r54
title: CIL: 52170, Homo sapiens. In Cell Image Library

description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
DOI: 10.6075/j0z89bdt
title: CIL:2720, 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 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.
DOI: 10.6075/j0j67g0x
title: CIL:8040, Mus musculus. In Cell Image Library

description: Fluorescence recovery after photobleaching (FRAP)kinetics of MeCP2 were recorded using a mouse fibroblast cell line stably expressing MeCP2-GFP. Live cells were imaged using a Zeiss LSM 510 meta confocal microscope with fluorescence excitation at 488 nm and a 63x plan-apo oil lens. The image series has 2 pre-bleach shots, one immediately after bleaching two 1 micrometer diameter circles of pericentromeric heterochromatin, followed by 122 images at 2 sec intervals.
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: quantity of GFP-protein
Visualization methods: Green fluorescent proteins from Anthozoa
Processing history: unprocessed raw data
DOI: 10.6075/j05m64gd
title: CIL:11534, Macaca mulatta, melanocyte. In Cell Image Library

description: Figure 299 from Chapter 11 (Melanin Pigment) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Melanocyte pigment cell from the iris in the eye of the Macaca mulatta. The cytoplasm is crowded with melanosomes, all limited by a membrane. Image by Giuseppina Raviola. 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
Visualization methods: osmium tetroxide
Data qualification: Processed
DOI: 10.6075/j0x929f7
title: CIL:9856, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: In mitosis the nuclear envelope of the micronucleus becomes heavily and uniformly labeled with anti-b-tubulin which is not in the form of microtubules. Some tubulin is also present inside the micronucleus. Apparently b–tubulin is being recruited to the mitotic micronucleus to form the spindle inside the intact micronucleus. Microtubules are present in the cytosol. TEM taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 7,900X. Bar = 1µm. 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 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:38688) is in the library and available 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; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j04m94db
title: CIL: 54787, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Nestin staining
DOI: 10.6075/j08k7996
title: CIL: 54891, Saccharomyces cerevisiae, Single cell. In Cell Image Library

description: Preparation: Image was captured at a magnification of 6600X on electron microscope film, then enlarged an additional 3.25X when printed onto photographic paper and scanned at 600 dpi.
Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Uranyl acetate; phosphotungstic acid
description: Miller chromatin spread. For yeast technique see: Osheim YN, French SL, Sikes ML, Beyer AL. Electron microscope visualization of RNA transcription and processing in Saccharomyces cerevisiae by Miller chromatin spreading. Methods Mol Biol. 2009;464:55-69. doi: 10.1007/978-1-60327-461-6_4. PMID: 18951179.
description: Part of a collage of images of a single nucleolus from yeast strain NOY1051 which has a fixed rDNA array size of 143 repeats. In total 71 of 120 35S ribosomal RNA genes visualized in the Miller chromatin spread from this cell are transcriptionally active. An overview of this nucleolus photographed at low magnification is published in French et al. (2008) Mol Cell Biol. 28:4576-87, Fig. 3A. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447126/figure/f3/
DOI: 10.6075/j06h4g17
title: CIL:39077, Triticum sp., leaf. In Cell Image Library

description: Leaf segments 1 cm from the tip were fixed with 2% glutaraldehyde, postfixed with 1% osmium tetroxide, dehydrated, and embedded in Spurrs resin. Thin sections were stained with uranly acetate and lead citrate and examined in a JEOL 100C transmission EM at 60 KV, and images recorded on film. See Fig 5 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: Wheat seeds were germinated and grown for 6 days in the dark, greened at high light intensity for 4 days, then prepared for thin section electron microscopy. This chloroplast from a wild-type plant shows the characteristic grana stacks of thylakoids (GT) and unstacked stromal regions (ST). Also seen are osmiophilic globules (PG). This set of grouped images, which also shows freeze-fracture views, includes the chlorophyll b-deficient CD3 mutant.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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; lead salt; osmium tetroxide
Data qualification: Processed
DOI: 10.6075/j0m61jkq
title: CIL:39782, Lytechinus pictus, embryonic cell. In Cell Image Library

description: Images taken on a JEOL 35C SEM. 
Processing protocol:
1. 2% GTA in 75% MBL SW or FilteredSW 
FSW - fix for 1.5hrs. RT.
2. Rinse with 0.1M NaCacodylate buffer pH 7.4
3. 0.5% OSO4 in .075M NaCacodylate buffer pH 7.4 - 30' in the cold
4. Rinse in 0.1M NaCacodylate buffer ph 7.4
5. Dehydrate thru ETOH: 30%, 50%, 70%, 95% for 5 min each
6. 100% - 3 changes - 15' each
7. Critical Point Dry
8. Stick embryos down onto silver paint. Gently crack open with glass needle (pipette drawn out to a fine point).
9. Sputter coat with AuPd.
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: gold; visualization of contiguous regions; osmium tetroxide
Processing history: unprocessed raw data
description: Scanning electron microscope image of Lytechinus pictus [sea urchin] embryo at the 2-cell stage. The fertilization envelope has been removed to reveal the cells covered with a dense meshwork of the hyaline layer, in which microvilli are embedded.This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
DOI: 10.6075/j0r49pqr
title: CIL:36637, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: This cell was exposed to HRP for 30 seconds and then chased in HRP-free medium for 3 minutes. The subsequent incubating with hydrogen peroxidase and diaminobenzidine resulted in an electron opaque reaction product in the peroxisomes not because they took in HRP but because the peroxisomes contain large amounts of catalase that results in the reduction of hydrogen peroxidase. This was followed by standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Like other cells Paramecium has peroxisomes. These organelles are usually smaller than mitochondria and have a granular appearance and contain a few tubular-like inclusions. These tubules have not been conclusively shown to be continuous with the single limiting membrane of this organelle. In this case the peroxisome has a microtubule lying along its surface. This cell was exposed to HRP for 30 seconds and then chased in HRP-free medium for 3 minutes. The subsequent incubating with hydrogen peroxidase and diaminobenzidine resulted in an electron opaque reaction product in the peroxisomes not because they took in HRP but because the peroxisomes contain large amounts of catalase that results in the reduction of hydrogen peroxidase. HRP can only enter the living cell by endocytosis, phagocytosis, when trichocysts are discharged, at the open cytoproct or when a CV opens. TEM taken on 6/13/79 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 22,500X. Bar = 0.25µm.
DOI: 10.6075/j0086510
title: CIL: 53958, Homo sapiens, HeLa. In Cell Image Library

description: RGC 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: 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.
DOI: 10.6075/j0j102mn
title: CIL: 51198, 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: 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
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.
DOI: 10.6075/j0wh2q3g
title: CIL:39634, Saccharomyces cerevisiae. In Cell Image Library

description: 10-hour timelapse of the double mutant Clb2dbŒî, Clb5Œî, which has the destruction box region of the CLB2 gene, on the cell cycle control system in budding yeast. The yeast, Saccharomyces cerevisia, are growing in 2% raffinose, since this mutation is inviable in glucose. The images from two experiments done with Wild-type Saccharomyces cerevisiae as a control 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.
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.
DOI: 10.6075/j0th8kvb
title: CIL:12107, Colpoda cucullus, 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 to Photoshop.
Data qualification: Processed;spatialmeasurements
description: A tangential view through a dikinetid shows two microtubular ribbons extending toward the pellicle, one from each basal body, and how they overlap with ribbons from other basal bodies under the pellicle. The peroxisome has one membrane but is filled with numerous tiny circular profiles that may represent tiny tubules. These tubules are much smaller than the membranous cristae in the mitochondria and are more probably proteinaceous in composition. TEM taken on 6/3/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:2862) 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 were prepared at approximately 75nm thickness. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).