cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.rdph77
title: Occurrence Download

description: A dataset containing 47945 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cyperus prolixus, Cyperus pseudokyllingioides, Cyperus pseudovegetus, Cyperus pumilus, Cyperus reflexus, Cyperus retroflexus, Cyperus retrorsus, Cyperus richardii, Cyperus rigens, Cyperus rigens rigens, Cyperus laevigatus laevigatus, Cyperus rotundus, Cyperus sanguinolentus, Cyperus schweinitzii, Cyperus serotinus, Cyperus sesquiflorus, Cyperus sphacelatus, Cyperus squarrosus, Cyperus stoloniferus, Cyperus strigosus, Cyperus subsquarrosus, Cyperus surinamensis, Cyperus filicinus, Cyperus tenuiculmis, Cyperus erythrorhizos, Cyperus tenuispica, Cyperus trialatus, Cyperus trinervis, Cyperus tuberosus, Cyperus unioloides, Cyperus victoriensis, Cyperus virens, Cyperus vorsteri, Cypretta dubiosa, Cypretta globula, Cypretta seurati, Cypretta turgida, Cyprinella analostana, Cyprinella galactura, Cyprinella lutrensis, Cyprinella pyrrhomelas, Cyprinella spiloptera, Cyprinella venusta, Cyprinella whipplei, Cyprinion acinaces, Cyprinodon diabolis, Cyprinodon eremus, Cyprinodon macularius, Cyprinodon macularius macularius, Cyprinodon nevadensis)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 },
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 47945 records from 334 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014693-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0736qrg
title: CIL: 54673, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after αSNAP KD, 28uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocytes after disruption of cortex glial morphology. After knockdown of αSNAP, a protein part of the vesicual transport pathway, we observed aberrant infiltration by astrocytes into the cortex.
DOI: 10.6075/j0k35swt
title: CIL:1041, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 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: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j0b857kq
title: CIL: 51770, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.15468/dl.2fs5eq
title: Occurrence Download

description: A dataset containing 69676154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.85666 40.21549,-72.00013 40.21549,-72.00013 42.5397,-74.85666 42.5397,-74.85666 40.21549))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 69676154 records from 1114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009235-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0ff3s2h
title: CIL: 53939, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: 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
DOI: 10.6075/j0ks6qgw
title: CIL:25396, Drosophila melanogaster, Salivary gland. In Cell Image Library

description: Salivary glands from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film, are transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. 

Image shows a series of bands and interbands in a polytene chromosome. This image was taken with a tilt angle of 55 degrees. The accompanying grouped image, taken at 45 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0rj4h7n
title: CIL:25378, Maize mosaic virus, Peregrinus maidis, secretory cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: recorded image
Data qualification: Raw;spatialmeasurements
description: Electron micrograph of Maize mosaic virus (MMV, Rhabdoviridae) in secretory cells from the principal salivary gland of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. In the principal salivary glands, MMV (arrows) buds through cytoplasmic membranes. Abbreviations: ics, intercellular space; SV, secretory vesicles. The accompanying image in this image group contains labels and scale bar. 
 
Methods: Dissected insect organs were processed for TEM by fixation in glutaraldehyde and osmium tetroxide and embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM.

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.
DOI: 10.6075/j0dz072m
title: CIL:25376, Maize mosaic virus, Peregrinus maidis, neuron. In Cell Image Library

description: Electron micrograph of Maize mosaic virus (MMV, Rhabdoviridae) in nerve axons of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. In many cells, MMV buds through nuclear membranes and accumulates in perinuclear space. In nerve axons, and in prinicple salivary glands, MMV buds through cytoplasmic membranes. The accompanying image in this image group includes labels and scale bar. 
 
Methods: Dissected insect organs were processed for TEM by fixation in glutaraldehyde and osmium tetroxide and embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM.

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0g15zmp
title: CIL:25374, Maize mosaic virus, Peregrinus maidis, ganglion interneuron. In Cell Image Library

description: Electron micrograph of Maize mosaic virus (MMV, Rhabdoviridae) in nerve ganglion of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. MMV buds through nuclear membranes and accumulates in perinuclear space in cells of the nerve ganglia. The accompanying image in this image group includes labels and scale bar. 
 
Methods: Dissected insect organs were processed for TEM by fixation in glutaraldehyde and osmium tetroxide and embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM.

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j02j6bzj
title: CIL:40186, Homo sapiens. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: Single computed slice through a tomographic reconstruction of a lamellar structure observed in HeLa cells transfected with mutant connexin 50, imaged using intermediate voltage electron microscopy, and labeled using the tetracysteine-ReHAsH system and fluorescence photoooxidation. The concentric double membrane layers of the aggregate appear to form "onion skin" sheets that do not form a closed structure along the long axis. The differential staining between the outside and inside is most likely due to impeded diffusion of DAB into the interior of these accumulations. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information see: Lichtenstein et al. The cytoplasmic accumulations of the cataract-associated mutant, Connexin50P88S, are long-lived and form in the endoplasmic reticulum Exp Eye Res. 2009 Mar;88(3):600-9. PMID: 19073179
description: ReAsH-labeled cells were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate, pH 7.4 at 4°C. After 20 min, the cells were rinsed in 0.1 M cacodylate pH 7.4 and incubated for 30-45 min with blocking buffer (10 mM KCN, 10 mM aminotriazole, 0.01% hydrogen peroxide/50 mM glycine in 0.1 M cacodylate pH 7.4). This buffer was then replaced with 1 mg/ml diaminobenzidine (DAB) in blocking buffer, and photoconversion was performed using intense illumination (75 W xenon arc lamp without neutral density filters) focused through the microscope objective. Rinsing and further preparation of the sample for transmission electron microscopy were performed as described in Gaietta et al. (2002). Sections were stained with uranyl acetate prior to acquisition of the tilt series.
DOI: 10.6075/j0ns0t97
title: CIL: 50844, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Treated cells were cultured in YPD medium and 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: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Saccharomyces cerevisiae cells (S228C background) were treated with 0.5 mM of sodium arsenite for 60 minutes. Then, samples were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
DOI: 10.6075/j0cv4gq6
title: CIL:36217, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A view of the cortex showing early endosomes are often cup shaped and can have several coated evaginations arising from the rim of the cup. TEM taken on 8/10/65 by R. Allen with RCA EMU3F operating at 50kV. Neg. 12,700X. Bar = 0.5µm. 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: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j06973sm
title: CIL:55765, 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: Control cells.
DOI: 10.6075/j0sb44x9
title: CIL:10462, Toxoplasma gondii RH. In Cell Image Library

description: Toxoplasma gondii expressing EGFP tagged Tgbeta2-tubulin and mCherry-TgDCCP (Double cortin containing protein), an unpublished microtubule binding protein. Images overlaid with DIC. For GFP, ex 450-490 em 500-540; for mCherry ex 555-592 em 600-665. Images acquired using API Delta Vision on a Olympus ix70 wide-field microscope. Objective: Olympus 60X water immersion, 1.2 NA. Captured with CoolSnapHQ/ICX285. 19 images in z-series; this is raw data corresponding to deconvolved stack: CIL# 10463.
Image is a control not treated with oryzalin. Part of an experiment with oryzalin-treatment. 
Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; boundaries between regions with different refractive index
Visualization methods: EGFP; mCherryFP
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0pn955x
title: CIL: 52544, 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=7, y=1, z=15 from BL32077_Myc_Terc