cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0qz29sd
title: CIL:36969, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #2 (day 2) of a time lapse series contained with in this image group. It is a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 The images were acquired daily over 3 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j0r78dz7
title: CIL: 54257. In Cell Image Library

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: TKL 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
DOI: 10.6075/j0833rkt
title: CIL: 52443, 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: Tile x=5, y=3, z=19 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
DOI: 10.6075/j0kk9b3g
title: CIL:40119, Homo sapiens, HTLV-1 subtype A, mature CD4 single-positive thymocyte, T cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
description: A single computed slice through a tomographic reconstruction of a virological synapse formed between naturally HTLV-1 infected CD4+ T cells and autologous uninfected CD4+ target cells. HTLV-1 particles in the synaptic cleft were identified by immunolabeling using anti-Gag p19 labeling and peroxidase-DAB detection. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information see: Majorovits et al. (2008) Human T-Lymphotropic Virus-1 visualized at the virological synapse by electron tomography. PLoS ONE 3: e2251, doi:10.1371/journal.pone.0002251, PMID 18509526
description: CD4+ T cells were isolated and cultured overnight to allow spontaneous expression of HTLV-1 proteins, and subsequently prepared for EM. To detect HTLV-1 Gag matrix protein in infected cells the samples were labelled against HTLV-1 Gag p19 (Tanaka et al., 1986) using the DAB kit from Molecular Probes (Invitrogen Ltd, Paisley, UK ). After the PFA/glutaraldehyde fixation, the samples were incubated in PBS containing 1% BSA, 0.1% Triton X-100 and 2% H2O2, for 1 h at 37uC to block non-specific antibody binding and to quench the endogenous peroxidase activity of the cells. To detect the HTLV-1 complexes, the cells were incubated with 5 mg/ml of anti-Gag p19 (GIN7 mAb) [33] diluted in PBS 1% BSA, for 1 h at 37uC. Then the second antibody, anti-Mouse mAb conjugated to HRP (Invitrogen Ltd, Paisley, UK ), was added at a final dilution of 1 mg/ml, and incubated for 30 minutes at 37uC. The cells were washed three times with PBS containing 1% BSA between each step. For detailed methods of the preparation, refer to the CCDB link provided.
DOI: 10.6075/j0vt1qxn
title: CIL:35983, Rattus, fat cell. In Cell Image Library

description: Figure 362 from Chapter 15 (Cytoplasmic Inclusions) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Portions of two adipose cells and associated connective tissue from the epididymal fat pad of a rat. Newly synthesized lipid first forms small droplets in th peripheral layer of the cyoplasm (arrows) before merging with the large central drop. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs 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/j0c53khg
title: CIL: 53627, Homo sapiens, HeLa. In Cell Image Library

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
description: Atypical 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/j0gh9gsg
title: CIL:39070, Mus musculus, epithelial cell. In Cell Image Library

description: B0007543 Kidney cortex. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: This light micrograph shows a transverse section of a region of mouse kidney cortex stained with toluidine blue. The kidney is made up of two distinct tissue regions: the medulla and the cortex. The nephrons are the functional units of the kidney and produce urine; they span both the medulla and the cortex. The medulla is the inner most region and contains the part of the nephron called the loop of Henle that is involved in the reabsorbtion of water. The cortex is present around the outside of the medulla and contains regions of the nephron called the proximal and distal convoluted tubules and glomerulus. This is where blood is filtered and the balance of irons and nutrients is maintained. In this image, the top left hand corner shows about a quarter of a Bowman's capsule, with capillaries and sections of red blood cells. The right hand side shows a cross section of a proximal convoluted tubule (PCT). The epithelial cells that form its walls are full of mitochondria. The PCT is also fringed with microvilli extending in to the lumen of the tubule, which greatly increase the surface area for absorption.
description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: toluidine blue
DOI: 10.6075/j0qc02q0
title: CIL:1314, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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
description: High resolution view during division showing the micronucleus contains internal microtubules as well as a layer of b-tubulin, not in microtubular form, on or just inside the nuclear envelope. The section is immunogold labeled with anti-b-tubulin. TEM taken on 7/8/96 by R. Allen with Zeiss 10A operating at 60kV. Neg. 19,800X. 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/).
DOI: 10.6075/j0610z1p
title: CIL:13885, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa tem1::GAL-UPL-TEM1-TRP1 pRS316::eGFP-TEM1) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
description: Tem1 normally localizes preferentially to the spindle pole body (SPB) that enters the daughter cell during anaphase (this image and CIL# 13882). This image shows SPB localization of eGFP-Tem1 (eGFP, green) in anaphase cells. tem1Δ::GAL-UPL-TEM1 cells expressing eGFP-TEM1 from a CEN plasmid were grown on 2% raffinose/2% galactose and transferred to 2% glucose medium prior to image capture. Nuclear morphology was assessed by DAPI (blue). A differential interference contrast (DIC) image is also shown (gray). The tem1Δ::GAL1-UPL-TEM1 strain allows for the rapid, conditional depletion of Tem1. UPL, which stands for ubiquitin-proline-LacI, acts as a destabilizing module that permits rapid degradation of appended proteins. Image is Fig 1B, top panels, in J Cell Biol. (2011) 192: 599-614. Other images in Fig 1 include CIL #13882, 13883, 13884, 13885, 13886, 13887.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0f18xg9
title: CIL:11805, Danio rerio, yolk syncytial layer cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Morphogenesis of the ventral yolk syncytial layer (YSL) from sphere stage to the end of gastrulation. The last round of nuclear division occurs before marginal band contraction and epiboly begins. As convergence occurs toward the dorsal side, a divergence of YSL nuclei from the ventral midline can be seen in this timelapse. As nuclei on the dorsal side extend up and through the animal pole, animal pole nuclei move ventrally and laterally. Video made available by Mark Cooper through Zebrafish - The Living Laboratory.
DOI: 10.6075/j0154gq6
title: CIL: 53767. In Cell Image Library

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
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.
DOI: 10.6075/j0pg1r8j
title: CIL: 52401, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=5, z=19 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/j0qz291j
title: CIL:6261, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

The image was recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6262.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0mc9007
title: CIL:35626, 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; differences in amount of elastic light scattering
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cln2. Cln2 is a G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p).These phase,gfp images are part of an image group that ranges from CIL:35620-35639. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
DOI: 10.6075/j0ms3sgw
title: CIL: 53802, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: NDK 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/j0jm287t
title: CIL:48836, Mus musculus, MC57-Cerulean. In Cell Image Library

description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC57-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the DsRed mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts (absent in the DsRed mouse tumor). Image name: 120513 parab dsred tumor flank.lif - 6 

Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
description: Item type: confocal microscopy
DOI: 10.6075/j01j9929
title: CIL:39765, Mus musculus, cardiac muscle cell. In Cell Image Library

description: Transmission electron micrograph of mouse atrial cardiac muscle showing a close up image of the intercalated discs, which support synchronized contraction of the cardiac muscle.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
description: Primary fixation included: 2.5 % glutaraldehyde, 2% formaldehyde in 0.1 M Na-phosphate buffer, pH 7.4. Post-fixed in 2% OSO4 in 0.1 M Na-phosphate buffer, pH 7.4. Stained en bloc in 1% uranyl acetate. The tissue was then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph image was taken using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80kV.