cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.22favf
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Scutellaria scordiifolia"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009656-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j07d2t81
title: CIL:10436, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes, as shown in this micrograph. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide 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
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j07m0789
title: CIL:39171, 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: The figure shows the beginning of the cytopharyngeal ribs of the ribbed wall. The peristome is bordered on one side by the paroral kinety that has 2 rows of basal bodies, of which only one is ciliated. The peristome is a deep funnel shaped indentation that leads to the cytostome and on to the nascent food vacuole forming region. Also seen are the oral polykineties and the perioral kineties. TEM taken on 6/13/69 by R. Allen with Philips 300 operating at 60kV. Neg. 4,270X.
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. 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/j0057fnq
title: CIL: 54410, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: 17.2 degrees ℃
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 17.2 degrees Celcius
description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
DOI: 10.6075/j0pr7tb9
title: CIL: 54839, Conchiformibius steedae, bacteria. In Cell Image Library

description: Leica TCS SP8 X; 63X Plan-Apochromat glycerine objective with a NA of 1.30 and a refraction index of 1.46.
description: Imaging mode: confocal microscopy
Visualization methods: fluorescent d amino acids
description: C. steeade septum after consecutive incubation with BADA for 30 minutes and TADA for 30 minutes. Front view of the 3D reconstruction.
DOI: 10.6075/j0sq8zmh
title: CIL:1621, 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 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
DOI: 10.6075/j0tb16wv
title: CIL:10362, Rattus, multipolar neuron. In Cell Image Library

description: Cultured hippocampal neurons after 17 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red) but not axons, which are not apparent in the immunofluorescence channel. Both axons, and dendrites, can be seen in the hidden phase micrograph which can be turned on using the edit function in the detailed viewer. Neurons at 10, 14, and 17 days in vitro are represented in this image group. 

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 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). 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. A multilayer stack of the fluorescent image of MAP2 staining and the phase image was generated using MetaMorph.
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
DOI: 10.15468/b5frax
title: Fossil Collection (MHNG-GEPI) of Muséum d'histoire naturelle de Genève
DOI: 10.6075/j0nk3czf
title: CIL:36667, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The body of the trichocyst is composed of a core and a cortex which have slightly different electron diffracting properties, thus the cortex is darker since it scatters more electrons. An electron transparent zone surrounds the cortex and separates the trichocyst membrane from the body. The trichocyst tip is composed of a central spike covered by a sheath. The spike is nail-shaped with its ‚Äúhead‚Äù resting on the trichocyst body. The trichocyst membrane completely surrounds both trichocyst body and sheath. (Details of trichocyst fine structure were recorded by Bannister, J. Cell Sci. 11:899-929, 1972.) TEM taken on 4/6/78 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 14,750X. Bar = 0.5µm.
description: 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; 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/j06d5t3m
title: CIL:39594, Saccharomyces cerevisiae. In Cell Image 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.
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 electrons
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 TEM1. 
 
 TEM1 is a GTP-binding protein of the ras superfamily involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis. 
 
These phase,gfp z-series images are part of an image group that ranges from CIL:39591-39595. 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/j0d799fj
title: CIL:2644, 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: 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 12 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/j01r6qbs
title: CIL:36850, 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: 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 #11 (second time-lapse set, 30 minutes) of a time lapse series contained with in this image group. It shows neurons 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.
 
 These cells were 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.
DOI: 10.6075/j02n52gm
title: CIL:55768, Homo sapiens, HEK293BR. In Cell Image Library

description: Imaging mode: Apotome Microscopy
Visualization methods: Immunofluorscence staining
description: Immunofluorescence staining with primary and fluorescence-tagged secondary antibody.
description: Treatment with both Bafilomycin and PMA.
DOI: 10.6075/j0x34wsf
title: CIL:40338, sildalcea malviflora, pollen. In Cell Image Library

description: Preparation: acetolysis
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
Processing history: unprocessed raw data
description: Scanning electron micrograph of sildalcea malviflora (prairie hollyhock) pollen. These specimens have been acetolyzed to remove cytoplasm and pollenkit in order to reveal the intricate wall structure. This is part of a large image collection of scanning electron micrographs of pollen samples. Images of a particular species are grouped together. However, to find images and groups of images from other species, please search for the the name of the contributor, Louisa Howard.
description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
DOI: 10.6075/j0nk3df4
title: CIL:44504, Canis lupus familiaris, kidney epithelial cell. In Cell Image Library

description: Madin-Darby Canine Kidney (MDCK) epithelial cells expressing YFP-membrane were maintained in DMEM supplemented with 5% fetal FCS in a 37°C, 5% CO2 incubator.
Wound healing assay: Cells were grown to 90% confluence in 24-well plates. Prior to scratching, the cells were starved by changing the medium to DMEM plus 0.1% FCS (starvation medium) for 24 hours. The medium was then changed to either fresh starvation medium (control), or starvation medium with 80 ng ml-1 HGF/SF for an additional 2 hours. A scratch of approximately 300 μm in width was generated using a 200 μl tip. The plate was subjected to time lapse microscopy in a stage incubator (OKOLAB, Italy) on a computer-controlled motorized stage of a confocal microscope (CLSM-510, Carl Zeiss, Germany), used in non-confocal DIC mode, with a 10x (NA 0.30) objective. Image acquisition was initiated 2 hours post scratching. Images were acquired every 15.7 minutes for 15 hours. The coordinates of each scratch were predefined, and a macro that repetitively positions the field of view at each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence was used for the analysis.
description: Time series light microscopy images illustrating a wound healing assay. A monolayer of MDCK (Madin-Darby Canine Kidney) epithelial cells is scratched to create a 'wound' about 300 micrometers in width, after which the growth of the cells to fill the wound is monitored by recording images over the course of 15h.This image is part of a group of 12 that includes control cells (CIL:44501, 502, 506, 507, 508) and after addition of Hepatocyte Growth Factor /Scatter Factor (HGF/SF) to activate HGF/SF-Met signaling (CIL:44503, 504, 505, 509, 510). Also in the group are two movies, one control (CIL:44511), and one HGF/SF treated (CIL:44512). For additional wound healing assays see CIL:43401 and images grouped with it.
description: Preparation: living tissue
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: 10.15468/dl.ekdxke
title: Occurrence Download

description: A dataset listing the 558 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is South America",
 "Country is Peru",
 "Geometry POLYGON((-71.61392 -13.21795,-71.58236 -13.18348,-71.56667 -13.11305,-71.41959 -12.58844,-71.27806 -12.5631,-71.26917 -12.5053,-71.21137 -12.4386,-71.18024 -12.32597,-71.10169 -12.44305,-71.01573 -12.39711,-70.79152 -12.21778,-71.21917 -11.74475,-71.30358 -11.43116,-71.60885 -11.22765,-72.1532 -10.96195,-72.19623 -11.00504,-72.19623 -11.06703,-72.13673 -11.11987,-72.21255 -11.14856,-72.22467 -11.33079,-72.28205 -11.34616,-72.32155 -11.56819,-72.36766 -11.59073,-72.4434 -11.72308,-72.38551 -11.78712,-72.407 -11.8235,-72.35679 -11.85937,-72.35167 -11.93416,-72.33966 -11.97446,-72.27959 -12.00623,-72.27844 -12.06862,-72.11324 -12.09114,-72.11135 -12.24402,-71.97325 -12.33044,-71.97325 -12.37781,-72.04603 -12.40034,-72.09166 -12.49133,-72.07318 -12.51732,-72.01195 -12.56815,-71.96163 -12.64848,-71.98884 -12.67635,-71.97323 -12.69509,-71.95334 -12.69686,-71.9219 -12.70355,-71.92168 -12.72206,-71.90294 -12.73566,-71.91298 -12.73878,-71.92435 -12.75484,-71.91195 -12.77527,-71.88274 -12.79557,-71.90638 -12.81987,-71.8872 -12.84976,-71.85667 -12.90785,-71.79145 -12.95935,-71.77094 -12.98165,-71.78588 -12.99235,-71.78409 -13.00417,-71.71795 -13.08268,-71.66019 -13.14913,-71.64168 -13.15426,-71.63856 -13.16162,-71.63165 -13.19239,-71.61392 -13.21795))",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Mammalia, Amphibia, Aves, Crocodylia, Squamata, Testudines)"
 ]
}

 The dataset's 558 records were derived from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009644-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j09023zs
title: CIL:48056, Macaca mulatta, kidney glomerular epithelial cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; lead citrate; uranyl acetate
Item type: X-ray micrograph
Imaging mode: transmission electron microscopy (TEM)
description: Transmission electron micrograph of segment of kidney cortex from a Rhesus monkey infused with 20% perfluorodecalin, 10% F68, 8 - 10 days after infusion at 50 cc/kg. Emulsion # 750519
DOI: 10.6075/j0bv7gb3
title: CIL: 53904, Homo sapiens, HeLa. In Cell Image Library

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: 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/j08c9wmz
title: CIL:57377. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j0sb463c
title: CIL:57340. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j0x34xt9
title: CIL:57337. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j0ht2pnx
title: CIL:57347. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j0g1616h
title: CIL:57281. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.