cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0wh2pq4
title: CIL: 54341, Homo sapiens, HeLa. In Cell Image Library

description: CAMK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
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/j0hh6hth
title: CIL:12593, Spiroplasma kunkelii, Dalbulus gelbus, epithelial cell, prokaryotic cell, procaryotic bacteria. In Cell Image Library

description: Electron micrograph of corn stunt spiroplasma (CSS) between 2 split layers of the basal lamina surrounding the filter chamber (part of the alimentary canal) and in the hemolymph of a vector leafhopper D. gelbus. Note the mainly pleiomorphic forms in host cells and the filamentous/spiral forms in the hemolymph. CIL:19131, from the same image group, is a labeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. Additional images from this contributor are available in the Library.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt
Data qualification: Processed
description: Detailed methods: Tissue was processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera).
DOI: 10.15468/dl.hc7t3c
title: Occurrence Download

description: A dataset containing 1139416 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-09-04",
 "EventDate is less than or equal to 2025-10-04",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1139416 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009173-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.20350/digitalcsic/17670
title: Identifying Spatial Patterns of Egg Nursery Habitat for a Demersal Shark in the Northwestern Mediterranean Sea: Conservation and Management Implications [Dataset]

description: Scyliorhinus canicula egg occurrence locations used in this study are available as a .csv file in the Data S2
DOI: 10.20350/digitalcsic/17671
title: Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus [Dataset]

description: 15 figuras y 10 tablas
DOI: 10.15468/dl.d2tjt5
title: Occurrence Download

description: A dataset containing 1205 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Thamnophis rufipunctatus"
 ]
}

 The dataset includes 1205 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009194-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0hh6jdj
title: CIL:132, Mus musculus, fibroblast. In Cell Image Library

description: NIH 3T3 cell transfected with EGFP-VASP. VASP is localized to the focal adhesions and is also present along the protruding leading edge. VASP only hightlights the portions of the periphery that are advancing forward, giving VASP a non-uniform distribution along the leading edge.
 
 Time series taken as a single confocal slice using a Zeiss LSM 510 confocal with a 100X 1.3 NA objective, 488 nm excitation and a 505-530 BP emission filter.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: non-linear methods
DOI: 10.6075/j0c82831
title: CIL:37290, Streptococcus pneumoniae, bacteria. In Cell Image Library

description: A transmission electron micrograph of a diplococcus (renamed Streptococcus in 1974) pneumoniae bacteria. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: 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: lead salt
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification 2000X.
DOI: 10.6075/j0qn65d7
title: CIL:37180, Rattus, kidney cell, glomerular capillary endothelial cell, podocyte. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue
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
description: Relevant citations: 
Kanwar, Y.S. and M.G. Farquhar. 1979. J. Cell Biol. 81:137-153.
Farquhar, M.G., S.L. Wisssig and G.E. Palade. 1961 . J. Exp. Med. 113:47-66.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification X19,000.
description: Transmission electron micrograph of rat kidney filtration barrier. Micrograph illustrates the basement membrane between fenestrated capillary endothelium and podocyte foot processes at intermediate magnification. The series of images in this group have particular historic and cell biologic importance for determining the role of the glomerular basement membrane in urinary filtration, especially the charge properties and size selectivity in retention of proteins in the circulation. The images here clearly show the glomerular filtration barrier. The study also elucidated the role of the basement membrane in some forms of nephrosis. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0vm4c3t
title: CIL:37003, 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: 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 #6 (50 minutes) of a time lapse series contained with in this image group. It shows the dendritic arbor of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with 10 minute intervals over one hour and 10 minutes 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.
DOI: 10.6075/j02r3rg5
title: CIL:36833, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #3 (day 2) 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. Autofluorescent pigment cells are visible in the superficial layers of the z-stack. 
 
 The images were acquired daily over 2 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
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/j0k35tgv
title: CIL:37014, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #4 (day 3) of a time lapse series contained with in this image group. It shows the dendritic arbor from a neuron ofthe optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. Autofluorescent pigment cells are visible in the superficial layers of the z-stack. 
 
 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
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/j0hq3z6r
title: CIL:41696, Cricetulus griseus, ovary. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: CHO cells at metaphase were treated with 50% D2O, fixed with glutaraldehyde, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranyl acetate and lead citrate for HVEM observation at 1 MeV. See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High Voltage EM image of CHO metaphase chromosomes from a 'thick' section of metaphase-arrested cells treated with D20 to stabilize microtubules. This image was recorded with a specimen tilt of 45 degrees. The accompanying grouped image had a tilt of 55 degrees to create a stereo pair providing an oblique 3D view of the chromosomes.
DOI: 10.1594/pangaea.923103
title: OA and ripples metabolism data
DOI: 10.6075/j0bg2mw7
title: CIL:35529, Lilium longiflorum, gamete. In Cell Image Library

description: Illumination provided by a SpectraPhysics-Newport MaiTai laser with DeepSee dispersion compensation providing pulses of approximately 100 fs duration at 80 MHz. Wavelength set at 760 nm with emission at 465 to 50 nm.
Zeiss 710 multi-photon microscope with 63X N.A. 1.4 oil immersion objective. Pollen was removed from the flower, put in a coverslip bottom chamber, covered with tissue culture grade mineral oil, and imaged within 12 hours.
description: Lilium longiflorum (Easter Lily) pollen. This is a thin optical section through the center of the desiccated stage of the mature pollen showing autofluorescence or harmonic generation of intrinsic structures. The brightest signal is from the outer layer, the exine and raised pilae.
description: Preparation: unfixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: intrinsic mass distribution
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.1594/pangaea.923617
title: OA and ripples seawater chemistry data

description: In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2020-09-27.
DOI: 10.6075/j0bk1bpw
title: CIL:41707, Cricetulus griseus, ovary. In Cell Image Library

description: Cells were metaphase arrested with colcemid, then exposed to a low ionic strength medium (0.07M phosphate buffer)containing 50% D20 as a microtubule stabilizer. Preparations were squashed in 3:1 acetic acid:ethanol,stained, and transferred to an EM grid.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: Preparation: chemically fixed tissue
Relation to intact cell: squash
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High Voltage (1MeV) EM image of metaphase arrested CHO cell squashed in 3:1 acetic acid:ethanol and transferred to an EM grid. Portions of several chromosomes are seen. This micrograph was captured at a specimen tilt of 45 degrees. The accompanying image has a tilt of 55 degrees, creating a stereo pair that provides an oblique stereo view of the chromatids.
DOI: 10.6075/j0rv0n2n
title: CIL:41706, Cricetulus griseus, ovary. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: squash
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High Voltage (1MeV) EM image of metaphase arrested CHO cell squashed in 3:1 acetic acid:ethanol and transferred to an EM grid. Portions of several chromosomes are seen. This micrograph was captured at a specimen tilt of 45 degrees. The accompanying image has a tilt of 55 degrees, creating a stereo pair that provides an oblique stereo view of the chromatids.
description: Cells were metaphase arrested with colcemid, then exposed to a low ionic strength medium (0.07M phosphate buffer)containing 50% D20 as a microtubule stabilizer. Preparations were squashed in 3:1 acetic acid:ethanol,stained, and transferred to an EM grid.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
DOI: 10.1594/pangaea.983547
title: Vessel mounted ADCP current measurements (38 kHz) during RV METEOR cruise M188

description: Upper-ocean current velocities were measured along the track of the cruise M188 (March 7 - April 13, 2023) using a vessel-mounted acoustic current Doppler profiler (ADCP). The instrument was a Teledyne RD Instruments 38-kHz Ocean Surveyor, with the transducer was installed 5.0 m below the waterline. The instrument was operated in narrowband mode to achieve the maximum possible range. Velocity data were recorded in 100 16-m bins. The navigational data, as well as heading, pitch and roll data, were recorded together with the velocity measurements by the data acquisition software (VmDAS). The velocity data were converted into earth coordinates and averaged into one-minute intervals. A water track calibration was used (OSADCP_Toolbox) to determine misalignment angle (0.0°) and amplitude factor (1.000). The accuracy of the velocity data varies, and depends on the number of available good pings in each depth cell during one measurements interval.
DOI: 10.6075/j0kw5fdb
title: CIL:41486, Cricetulus griseus, epithelial cell. In Cell Image Library

description: CHO cells at metaphase were fixed with paraformaldehyde followed by OsO4, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranly acetate for HVEM observation.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High voltage (1MeV) transmission electron microscopy image of a 0.5 micrometer section through a Chinese hamster ovary cell at metaphase showing a chromatid pair, with kinetochores at the centromere. The image was taken with a specimen tilt of 37 degrees and is one of a group of 10 tilts from 77 degrees to 32 degrees at 5 degree intervals. Pairs of images provide oblique stereo views of the chromosome.
description: Preparation: formaldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0028qv2
title: CIL:40687, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: chemically fixed tissue; critical_point dried specimen
Relation to intact cell: isolated subcellular component
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High voltage (1MeV) transmission electron microscopy image of an isolated metaphase chromatid pair from a mouse A9 fibroblast, showing the fiber-like structure.
description: Cells in metaphase were exposed to 75 mM KCl, spread on water, picked up on grids, stained with uranyl acetate and critical point dried.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.