cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0959g96
title: CIL:26290, Saccharomyces cerevisiae. In Cell Image Library

description: Endoplasmic reticulum (ER) domains in 3D in a wild type S. cerevisiae cell (wt = BY4742) with a 371-nm bud. Domains are color coded as follows: Golgi (purple), and vesicles (30 nm is shown in pink, and 60 nm is shown in white), cecER and tubER (yellow and green), and pmaER alone (blue). Haploid cells were high pressure frozen and then freeze substituted with 0.1% uranyl acetate and 0.25% glutaraldehyde in anhydrous acetone, embedded in Lowicryl, and an 80-nm serial thin sections and 200-nm serial semithick sections were cut with an ultramicrotome. Dual-axis tilt series were collected from the samples from +/-60° with 1° increments at 300 kV using SerialEM (Mastronarde, 1997) at 300 kV using a field emission gun (Tecnai 30; FEI). Tilt series were recorded at a magnification of 23,000× using SerialEM (Mastronarde, 2005). After 2x binning on the recording 4098 x 4098–pixel charge-coupled device camera (Megascan 795; Gatan, Inc.), this magnification creates a 2000 x 2000–pixel image with a pixel size of 1.02 nm on the specimen. The nominal resolution in our tomograms was ~4 nm, based upon section thickness, number of tilts, tilt increments, and tilt angle range (Crowther relation; Koster et al., 1997). The IMOD package (Kremer et al., 1996) and its newest viewer, 3DMOD 4.0.11, were used to construct individual tomograms. Videos were made in 3DMOD and assembled in QuickTime Pro 7. Bar is 200 nm. Video relates to Figure 2 and Video 1 of J Cell Biol 2011 193:333-346.
description: Preparation: high pressure freezing; freeze substitution
Relation to intact cell: microtome-sectioned tissue
Item type: portrayed image
Imaging mode: transmission electron microscopy (TEM); tilt series; tomogram
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: surface rendering; volume rendering
DOI: 10.6075/j0xk8dpn
title: CIL:9168, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Sialyl Transferase-EGFP transfected HeLa cells demonstrating the redistribution of the Golgi Apparatus to the Endoplasmic Reticulum upon treatment with Brefeldin A (BFA). 
Images were collected as a 4D time series (z-stack over time). z-stacks of 48 individual timepoints are included in this collection of files as well as the movie SiEGFP_BFA.avi, which is the maximum projection of the z-stacks at the individual time points.

BFA was added according to the following protocol:
Timepoint1: Before addition of BFA 0seconds (8 Z-slices at 1 um apart)
Timepoint2: After addition of BFA 130seconds (8 Z-slices at 1 um apart) 
Timepoint3: 238 seconds (11 Z-slices at 1 um apart) 
Timepoint3 thru Timepoint48: Images captured every 5 seconds (11 Z-slices at 1 um apart at each time point) 

Images were collected on a Carl Zeiss spinning disk confocal with a 63X 1.4 NA objective with 250 ms exposures at 5 s intervals.
description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j09z93qz
title: CIL:11422, unclassified Insecta, spermatid. In Cell Image Library

description: Figures 234 and 235 from Chapter 7 (Mitochondria) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. During spermiogenesis in insects, mitochondria fuse into a large spherical mass called the nebenkern. The upper and lower figures shown here represent successive stages of this process. Images by David Phillips. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
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
Data qualification: Processed
DOI: 10.6075/j0v124px
title: CIL: 54830, Alysiella filiformis, bacteria. In Cell Image Library

description: Imaging mode: phase contrast microscopy
description: Nikon Eclipse NI-U microscope equipped with a MFCool camera (Jenoptik).
description: S. muelleri filaments
DOI: 10.6075/j0zg6r44
title: CIL:36693, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A more extensive freeze-fracture view of the membranelles on the left side of the buccal cavity. Fractures of eighty or more basal bodies can be counted in each of the dorsal three rows of the dorsal peniculus. The fracture plane jumps down into the cilia for most of the ventral peniculus and only a short segment of the quadrulus next to the cytopharynx is exposed in this fracture plane. The ventral peniculus ends where the quadrulus approaches the dorsal peniculus and the ventral row of the dorsal peniculus ends about eleven cilia posterior to this. Only the quadrulus extends to the end of the buccal cavity (not shown). TEM taken on 12/15/75 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,000X. Bar = 2µm.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
DOI: 10.6075/j0765dxn
title: CIL: 53011, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 1, z=20 from SC_028
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 image
DOI: 10.6075/j0348k35
title: CIL: 54144. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TK 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/j0s46r1s
title: CIL:12332, 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; Negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: View of the packed layer of mitochondria just under the dorsal pellicle of Euplotes is prominent. A row of eight cilia can be seen along one kinety arising from round to oval depressions in the cell's surface. A grid bar was deleted on the left. TEM taken on 8/1/67 by R. Allen with Philips 200 operating at 60kV. Neg. 1,800X. Bar = 5µm. 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 scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image is available in the library (CIL:38869) that can be used for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.15468/dl.m59ke2
title: Occurrence Download

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

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009296-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0nv9h9m
title: CIL:2646, 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/j0b856vw
title: CIL:13692, Homo sapiens. In Cell Image Library

description: This is one of six images in Figure 6 in Apaja et al., JCB 2010 that shows the fate of various model membrane proteins, that are either folded or in the unfolded state at the plasma membrane, expressed in stable tetracycline-inducible Flp-In T-Rex HEK293 cell lines. The three model membrane proteins were chimeras of the CD4 surface receptor consisting of 1.) a C-terminally truncated CD4 that contained a flexible cytoplasmic linker (CD4tl), 2.) a CD4tl fused to the N-terminal DNA-binding domain of the wild type bacteriophage lambda repressor (CD4tl-lambda), and 3.) a CD4tl fused to a L57C mutant lambda repressor (CD4tl-lambdaC). The CD4tl-lambdaC cytosolic domain was largely in native state at 26°C but predominantly nonnative state at 37°C thus allowing the use of thermal shifts to follow the fate of unfolded proteins. To examine the post-endocytic distribution of CD4 chimeras, membrane proteins were labeled by CD4 Ab capture for 20 mins in live cells at 37°C and chased for 1 h in the absence of extracellular Ab before fixation and labeling with secondary antibody to localize the internalized CD4 chimeras (green). Lysosomes were marked by by LAMP2 antibody (red). Fluorescence micrographs were obtained by a confocal microscope (LSM510 or LSM710; Carl Zeiss, Inc.) equipped with a Plan-Apochromat 63×/NA 1.4 objective in multitrack mode. This single optical section shows that internalized CD4tl-lambda protein does not co-localize with lysosomes. A companion image in this group shows that CD4tl-lambda, however, does at least partly co-localize with endosomes, a property shared with other membrane receptors.
description: Preparation: crosslinking-fixative fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of epitope
Visualization methods: Alexa Fluor 488; Alexa Fluor 555
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j02r3rj2
title: CIL: 54804, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Spheroid imaging
description: Brightfield and DAPI imaging merged.
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
DOI: 10.6075/j0g160pc
title: CIL:37084, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #5 (8 hours) of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 Complete z-stacks were acquired of this neuron at a 2 hour interval over 8 hours. These images are part of this image group. This time lapse series shows the development of the neuron's dendritic arbor. The dendritic arbor exhibits morphological plasticity with branch additions, retractions and extensions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the 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.
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: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0q52np8
title: CIL:2634, 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 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.
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/j0jh3k7w
title: CIL:2633, 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 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.
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
DOI: 10.6075/j0c53jnv
title: CIL:26314, Saccharomyces cerevisiae. In Cell Image Library

description: Endoplasmic reticulum (ER) domains in 3D in a wild type S. cerevisiae cell (wt = BY4742) with a 1255-nm bud. Domains are color coded as follows: Golgi (purple), and vesicles (30 nm is shown in pink, and 60 nm is shown in white), cecER and tubER (yellow and green), and pmaER alone (blue). Haploid cells were high pressure frozen and then freeze substituted with 0.1% uranyl acetate and 0.25% glutaraldehyde in anhydrous acetone, embedded in Lowicryl, and an 80-nm serial thin sections and 200-nm serial semithick sections were cut with an ultramicrotome. Dual-axis tilt series were collected from the samples from +/-60° with 1° increments at 300 kV using SerialEM (Mastronarde, 1997) at 300 kV using a field emission gun (Tecnai 30; FEI). Tilt series were recorded at a magnification of 23,000× using SerialEM (Mastronarde, 2005). After 2x binning on the recording 4098 x 4098–pixel charge-coupled device camera (Megascan 795; Gatan, Inc.), this magnification creates a 2000 x 2000–pixel image with a pixel size of 1.02 nm on the specimen. The nominal resolution in our tomograms was ~4 nm, based upon section thickness, number of tilts, tilt increments, and tilt angle range (Crowther relation; Koster et al., 1997). The IMOD package (Kremer et al., 1996) and its newest viewer, 3DMOD 4.0.11, were used to construct individual tomograms. Videos were made in 3DMOD and assembled in QuickTime Pro 7. Bar is 200 nm. Video relates to Figure 2 and Video 6 of J Cell Biol 2011 193:333-346.
description: Preparation: high pressure freezing; freeze substitution
Relation to intact cell: microtome-sectioned tissue
Item type: portrayed image
Imaging mode: transmission electron microscopy (TEM); tilt series; tomogram
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: surface rendering; volume rendering
DOI: 10.6075/j0w37v2f
title: CIL:26313, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: high pressure freezing; freeze substitution
Relation to intact cell: microtome-sectioned tissue
Item type: portrayed image
Imaging mode: transmission electron microscopy (TEM); tilt series; tomogram
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: surface rendering; volume rendering
description: Endoplasmic reticulum (ER) domains in 3D in a wild type S. cerevisiae cell (wt = BY4742) with a 1095-nm bud. Domains are color coded as follows: Golgi (purple), and vesicles (30 nm is shown in pink, and 60 nm is shown in white), cecER and tubER (yellow and green), and pmaER alone (blue). Haploid cells were high pressure frozen and then freeze substituted with 0.1% uranyl acetate and 0.25% glutaraldehyde in anhydrous acetone, embedded in Lowicryl, and an 80-nm serial thin sections and 200-nm serial semithick sections were cut with an ultramicrotome. Dual-axis tilt series were collected from the samples from +/-60° with 1° increments at 300 kV using SerialEM (Mastronarde, 1997) at 300 kV using a field emission gun (Tecnai 30; FEI). Tilt series were recorded at a magnification of 23,000× using SerialEM (Mastronarde, 2005). After 2x binning on the recording 4098 x 4098–pixel charge-coupled device camera (Megascan 795; Gatan, Inc.), this magnification creates a 2000 x 2000–pixel image with a pixel size of 1.02 nm on the specimen. The nominal resolution in our tomograms was ~4 nm, based upon section thickness, number of tilts, tilt increments, and tilt angle range (Crowther relation; Koster et al., 1997). The IMOD package (Kremer et al., 1996) and its newest viewer, 3DMOD 4.0.11, were used to construct individual tomograms. Videos were made in 3DMOD and assembled in QuickTime Pro 7. Bar is 200 nm. Video relates to Figure 2 and Video 1 of J Cell Biol 2011 193:333-346.
DOI: 10.15468/dl.sqw5fk
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Helianthus tuberosus"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009298-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.