cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0p26xzb
title: CIL:36988, 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 #5 (40 minutes) of a time lapse series contained with in this image group. It shows a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with 10 minute intervals and show 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.
 
 Images were acquired every 10 minutes for 1 hour. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~1.5 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
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/j0gq6x48
title: CIL:40269, Sus scrofa domestica, kidney epithelial cell. In Cell Image Library

description: Time lapse movie of a porcine kidney LLCPK1 cell stably expressing EGFP-alpha tubulin. The movie shows microtubule behavior from early prophase through metaphase.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Data qualification: Processed
description: Cells were imaged using a Nikon Eclipse TE300 microscope with 100x phase NA 1.4 objective lens and spinning disk confocal head (Perkin Elmer) and images captured with a MicroMax cooled CCD camera.
Images were captured every 2 sec and are displayed at 7.5 frames/sec. 
See also:N Rusan and P Wadsworth 2005. Centrosome fragments and microtubules are transported asymmetrically away from division plane in mitosis.J Cell Biol 168:21-28.
DOI: 10.6075/j0bz65fc
title: CIL: 50702, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 3.6_Cell_3_Surface_Rendering. In Cell Image Library

description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
3.6_Cell_3_Surface_Rendering is a compressed (zipped) folder containing all files required to render the surface of the bundle. Also included is the ‘ProjectLog’ file produced by Slice and View acquisition software.
This file is a part of Dataset 3, comprised of files related to the Cell #3 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
DOI: 10.6075/j0251h1t
title: CIL:38902, Mus musculus, neuronal stem cell, oligodendrocyte, astrocyte. In Cell Image Library

description: Confocal micrograph of neural stem cells transplanted into mouse brain Mouse neural stem cells, labelled with green fluorescent protein, have been transplanted into the brain of a newborn mouse and are developing into oligodendrocytes and astrocytes.
description: Preparation: chemically fixed tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
description: B0006484 Confocal micrograph 2006 Collection: Wellcome Images. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0mp52pm
title: CIL: 50883, Saccharomyces cerevisiae (baker's yeast, budding yeast), Young S. cerevisiae cells. In Cell Image Library

description: The cell surface of exponentially growing Saccharomyces cerevisiae cells was labeled with biotin by incubating the cells with 0,5 mg/ml Sulfo-NHS-LC biotin (#21335, Thermo Fisher scientific) for 20 minutes at room temperature. Cells were grown in YPD, harvested prior saturation of culture, and washed in PBS + 0,5% glucose. Biotinylated cells were labeled with 17.5 ug/ml Streptavidin magnetic beads (#21344, Thermo Fisher scientific) for 1.5 hours followed by 3 x 15 min magnetic sorting with PBS + 0,5% glucose washes in between. Another two rounds of growth, streptavidin-labeling, and sorting was performed. The unbound daughter cells were recovered in YPD for 4 hours before high pressure freezing. Samples were high pressure frozen in a Wohlwend Compact 3 machine, followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
description: Young Saccharomyces cerevisiae cells were collected after separation of the old cells from the culture. Old cells were isolated with the use of Streptavidin magnetic beads and the remaining young population was high pressure frozen and visualized with the use of transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0cn73r5
title: CIL:36961, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

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.
description: This is IMAGE #1 (day 1) of a time lapse series contained with in this image group. It shows 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: 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
DOI: 10.15468/dl.usvk6p
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "InstitutionCode is one of (BPBM)",
 "TaxonKey is one of (Chiruromys vates [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 149 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009433-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j06w98zj
title: CIL:40984, Mus musculus, neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Yellow fluorescent proteins from Aequorea; Cyan fluorescent proteins from Aequorea; Red fluorescent proteins from Anthozoa
description: Montage image of a brain stem from a Brainbow transgenic mouse. In Brainbow mice, neurons randomly choose combinations of red, yellow and cyan fluorescent proteins, so that they each glow a particular color. This provides a way to distinguish neighboring neurons and visualize brain circuits. These are large caliber axons of the auditory pathway. First Prize, 2007 Olympus BioScapes Digital Imaging Competition.
 
 
 For additional details see: Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW.
 Nature. 2007 Nov 1;450(7166):56-62.
DOI: 10.6075/j0js9qf8
title: CIL:36295, Rattus, astrocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
description: Male Sprague Dawley rats, 2 weeks of age, were anaesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. lucifer yellow in 200mM KCl. The astrocytes were filled using a 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000
(Hercules, CA) attached to a Nikon E600FN
(Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60× oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injection of a protoplasmic astrocyte from the CA1 region of hippocampus of a 2 week old rat reveals highly ramified spongiform processes. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled as a maximum projection image.
DOI: 10.6075/j0f47nbv
title: CIL:1591, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 0 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: 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.
DOI: 10.6075/j0fj2gb1
title: CIL: 52870, 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: One z layer of a z-stack at the given tile position
description: Tile x=4, y=5, z=5 from PS11_167511L_Myc_Terc
DOI: 10.6075/j04x56xg
title: CIL:9905, Euplotes sp., 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
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;spatialmeasurements
description: An image of the transition from basal bodies to cilia within a portion of one of the oral membranelles of Euplotes. Parasomal sacs occur between the rows of basal bodies although these endocytic ports are not as evident in Euplotes as in other ciliates. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 7/29/67 by R. Allen with Philips 200 operating at 60kV. Neg. 28,000X. Bar = 0.2µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:9706) is available for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0js9pcz
title: CIL:36575, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0pn94h0
title: CIL:41912, Arabidopsis thaliana, parenchymal cell, epidermal cell. In Cell Image Library

description: Confocal micrograph of Arabidopsis thaliana (thale cress) seedling leaf with stomata (yellow mouth-like structures) and parenchyma cells. Confocal microscopy. Honorable Mention, 2009 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
DOI: 10.6075/j0nk3cs6
title: CIL:13383, Homo sapiens, mammary epithelium (MEC). In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
description: The nucleolus during mammary epithelial differentiation and early mammary tumorigenesis. Proliferating 3D cultures of MCF-10.B2 cells treated to activate ErbB2 were stained at day 20 with ANA-N antibody to detect nucleoli (green) and counterstained with DAPI to delineate nuclei (blue). The stack is presented as a projected image in Fig 1A (Day 20, ErbB2 of Meaburn and Misteli, 2008 J Cell Biol 180:39-50.
The z-series was recorded with a Zeiss LSM 510 META confocal microscope with a 63x 1.4 NA objective lens.
DOI: 10.6075/j0t72h99
title: CIL: 54806, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Brightfield and DAPI imaging merged.
description: Spheroid imaging
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
DOI: 10.6075/j0xd10zw
title: CIL:1720, Caenorhabditis elegans. In Cell Image Library

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 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: 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
DOI: 10.6075/j0qz29p2
title: CIL: 53930. 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/j0mc901p
title: CIL:10398, Rattus, multipolar neuron. In Cell Image Library

description: Cultured hippocampal neurons after 23 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red), and PSD95, a scaffolding protein concentrated in the postsynaptic density of excitatory synapses, particularly in dendritic spines (green). 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (from S. Halpain) with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch) and PSD95 (from NeuroMab, with Alexa488 conjugated secondary, excitation, 496, emission, 519, Invitrogen). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. The merged image was generated by creating a MetaMorph stack file.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; elastic scattering of photons
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Processed;spatialmeasurements