cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0vm49xr
title: CIL:35185, Danio rerio, early embryonic cell. In Cell Image Library

description: Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Processing history: projection; rotation
description: Eye of a 24 hr zebrafish embryo stained for paxillin (green) and laminin (red). Images made available by Mark Cooper thru The Zebrafish A Living Laboratory.
DOI: 10.6075/j0t153bv
title: CIL: 53881, 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/j05m65b1
title: CIL: 53143, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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=5 from SC_030
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0pr7v7c
title: CIL:1708, 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 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: 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/j0xd11cp
title: CIL: 53762, Homo sapiens, HeLa. In Cell Image Library

description: CMGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
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/j0q23zvk
title: CIL: 53512, Homo sapiens, HeLa. In Cell Image Library

description: AGC 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/j00r9p5z
title: CIL: 54552, Lilium longiflorum, reproductive cell (microsporocyte). In Cell Image Library

description: Feulgen stained light microscopy image collected using a bright field zeiss microscope, using a 100X, N.A. 1.4 Neuflar lens.
description: Imaging mode: light micrograph
Visualization methods: DNA specific contrast staining using Feulgen staining
description: Metaphase I in a diploid lily pollen mother cell. The nuclear envelope is gone and the 12 bivalents can be seen lined up on the metaphase I plate. Counting from the top left and moving to bottom right, the 9th and 10th bivalents overlap a little.
DOI: 10.6075/j0xg9r5d
title: CIL:35691, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
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: A time lapse experiment of Saccharomyces cerevisiae expressing GFP taggedMAD2. 
 
MAD2 is a non-essential gene that encodes a component of the spindle checkpoint. The spindle checkpoint delays the onset of anaphase in cells with defects in mitotic spindle assembly or in the attachment of chromosomes to the spindle microtubules. The checkpoint works by inhibiting the activity of the anaphase promoting complex, thereby preventing the degradation of several cell cycle regulators. Like other spindle checkpoint mutants, mad2 loss-of-function mutants are sensitive to benomyl and cannot delay cell division in response to spindle depolymerization. Mad2p forms a tight complex with another spindle checkpoint protein, Mad1p, throughout the cell cycle. Mad2p also forms a complex with Cdc20p, which activates the anaphase promoting complex, and Mad3p; the presence of Mad1p is required for the complex to form. Bub1p, Bub3p, Mad1p, Mad2p, Mad3p, and the protein kinase Mps1p act in a branch of the spindle checkpoint pathway that may prevent premature chromosome disjunction. A second branch involves Bub2p and Bfa1p, and may prevent cytokinesis prior to chromosome segregation. Homologs of Mad2p act in the spindle checkpoint in Xenopus (Xmad2) and human (MAD2L1 andMAD2L2.MAD2 was originally identified as the open reading frame YJL031C. However, it is now known thatMAD2 corresponds to the adjacent open reading frame YJL030W, while YJL031C encodes the geranylgeranyltransferase subunit Bet4p.
 
These phase,gfp images are part of an image group that ranges from CIL:35680-35699. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.6075/j0vt1s8z
title: CIL:48106, Rattus norvegicus, fetal cardiomyocyte. In Cell Image Library

description: Relation to intact cell: dispersed cells in vitro
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Data qualification: Processed
description: Rat cardiomyocytes were plated and stained for actin (in red), desmin (in green) to reveal the intermediate filament essential for the structural integrity and function of muscle, and DAPI (in blue) to label nuclei.
description: Plated rat cardiomyocytes were fixed and immunostained for actin (from Santa Cruz), desmin (from Sigma), and DAPI (from Life Technologies). Images were acquired with a 40X (Plan Fluor, NA 0.75) lens, SPOT RT Slider CCD camera and SPOT Basic image capture software. Image generated with the Image J color combine function.
DOI: 10.6075/j0k074cz
title: CIL:39612, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0tb163j
title: CIL:11922, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde 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: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j01c1wk9
title: CIL: 53921. In Cell Image Library

description: Visualization methods: confocal microscopy
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.
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/j0610z07
title: CIL:34903. In Cell Image Library

description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data
description: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
DOI: 10.6075/j0j67fn1
title: CIL:12017, Hypsophrys nicaraguensis, keratocyte. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy; speckle microscopy
Parameter imaged: elastic scattering of photons; fluorescence emission
Source of contrast: differences in amount of elastic light scattering; distribution of a specific protein
Visualization methods: Alexa Fluor 546; phalloidin; visualization of contiguous regions
Processing history: contrast, brightness, image combine
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Formation of an actin axle during the maturation of polarity. During maturation of the polarized form, the circular actin bands around the cell body transitioned to an actin axle along the cell rear. Phase-contrast and AF546-phalloidin FSM time-lapse video of a cell initiating motility and maturing. 30x real time (frames were collected at 3-s intervals and are displayed at 10 frames/s). Phalloidin was conjugated to AlexaFluor546 and cells were imaged in culture media (Leibovitz's L-15 medium without phenol red supplemented with 14.2 mM Hepes, pH 7.4, 10% FBS, and 1% antibiotic-antimycotic). Time-lapse phase contrast and epifluorescent images were acquired using an inverted microscope (Diaphot-300; Nikon) with a 60× NA 1.4 oil plan-Apo objective (Nikon). Images were acquired every 3 s with a 60× oil objective. All time-lapse images were collected with a cooled back-thinned CCD camera (MicroMax 512BFT; Princeton Instruments) with a 2× optovar attached using MetaMorph software version 6 (Molecular Devices). Corresponds to Fig. S3 and video 8 from JCB 178:1207-1221, 2007.
DOI: 10.6075/j0dn44rr
title: CIL: 53920, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
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.
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/j02r3r9x
title: CIL: 53165, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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 5, z=6 from SC_030
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0ms3s4d
title: CIL:39170, Opercularia [NCBITaxon:168247], Opercularia coarctata, 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: 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: Opercularia is named for a ciliated flap (operculum) that is adoral to the opening to the oral region. However, this operculum is pulled back into the body when the myonemes are fully contracted as in this figure. The cilia bordering the operculum arise from the perioral kinetids. TEM taken on 6/13/69 by R. Allen with Philips 300 operating at 60kV. Neg. 4,270X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0f18z7k
title: CIL: 52174, Homo sapiens. In Cell Image Library

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.
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.
DOI: 10.6075/j089150g
title: CIL:12026, Nephrotoma, Nephrotoma suturalis, primary spermatocyte. In Cell Image Library

description: Movie of meiosis I in primary spermatocytes of the crane-fly Nephrotoma suturalis that have been experimentally flattened. 
Time-lapse polarization microscopy using a Nikon 
Microphot SA, equipped for liquid crystal polarized light microscopy 
(LC-PolScope, CRi, Woburn Massachusetts) 60x/1.4 PlanApo oil immersion objective, 1.4 NA oil imm. condenser, with 2.0x zoom lens. Images captured every 30/60/90 sec for 2 hr 31 min using a QImaging Retigo EXi CCD camera. Raw images were processed using a 5-frame algorithm (Shribak and Oldenbourg, 2003). A movie of the time series is included in this grouped set.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: polarization microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: intrinsic birefringence
Visualization methods: relative retardation (retardance) measurement
Processing history: 5-frame algorithm