cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09s1qc5
title: CIL:39158, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. There is a high resolution version of this image in the library (CIL:) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Cross section of the oral region (buccal cavity) posterior to the vestibulum. The cytopharynx is beginning on the dorsal surface and the ribbed wall, peniculi and quadrulus are present on the right and left. The floor of the buccal cavity is bordered by the filamentous reticulum and an anarchic field of basal bodies is found where the endoral membranelle terminates. TEM taken on 1/31/74 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 6,150X.
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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0h994mb
title: CIL: 51142, 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: 10.6075/j0p849w9
title: CIL:2787, 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 8 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: 10.57760/sciencedb.30807
title: Tube formation assay
title: Tube formation assay

description: Quantitative analysis of the total tube length in the HUVEC tube formation assay (n=3). Quantitative analysis of the tube node number in the HUVEC tube formation assay (n=3).
description: Quantitative analysis of the total tube length in the HUVEC tube formation assay (n=3). Quantitative analysis of the tube node number in the HUVEC tube formation assay (n=3).
DOI: 10.6075/j0k073sx
title: CIL: 52341, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=3, y=2, z=1 from BL024199_Myc_Terc
description: One z layer of a z-stack at the given tile position
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
DOI: 10.6075/j0kd1xk1
title: CIL: 53693. 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: Visualization methods: confocal microscopy
description: CMGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.6075/j0vh5mg0
title: CIL:46009, Homo sapiens. In Cell Image Library

description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
description: Plate 26202 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
DOI: 10.15468/dl.ksv2qj
title: Occurrence Download

description: A dataset containing 177599 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Nepal, Bhutan, India, Bangladesh, China, Pakistan, Afghanistan, Myanmar)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Myxini, Petromyzonti, Elasmobranchii, Holocephali, Coelacanthi, Dipneusti, Polypteriformes, Acipenseriformes, Lepisosteiformes, Amiiformes, Osteoglossiformes, Elopiformes, Albuliformes, Notacanthiformes, Anguilliformes, Saccopharyngiformes, Clupeiformes, Gonorynchiformes, Cypriniformes, Characiformes, Gymnotiformes, Siluriformes, Esociformes, Salmoniformes, Osmeriformes, Stomiiformes, Ateleopodiformes, Aulopiformes, Myctophiformes, Lampriformes, Percopsiformes, Zeiformes, Gadiformes, Polymixiiformes, Beryciformes, Ophidiiformes, Batrachoidiformes, Syngnathiformes, Synbranchiformes, Pleuronectiformes, Atheriniformes, Cyprinodontiformes, Beloniformes, Mugiliformes, Gobiesociformes, Lophiiformes, Tetraodontiformes, Perciformes)"
 ]
}

 The dataset includes 177599 records from 426 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009366-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j06h4gtj
title: CIL: 50893, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Heat shocked Saccharomyces cerevisiae cells (38 oC for up to 90 minutes) were high pressure frozen and embedded in HM20 resin. Samples were then stained for Ubiquitin with the polyclonal antibody ab19247 (Abcam) and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events. The black gold particles represent the presence of Ubiquitin.
description: Heat shocked 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. For the immuno-EM, samples were blocked for 2 hours in 0.8% BSA with 0.1% fish skin gelatine. A 1:10 dilution of the primary antibody ab19247 (Abcam) was used and a 1:20 dilution of the secondary antibody anti-Rabbit IgG 10 nm gold (Cat#25108, Electron microscopy sciences). Finally, samples were post fixed in 2.5% glutaraldehyde for 20 minutes. 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
DOI: 10.57760/sciencedb.30814
title: Effect of CA polysaccharide on cell migration
title: Effect of CA polysaccharide on cell migration

description: Representative images of GES-1 migration in the scratch wound healing assay at 0 h, 12 h, and 24 h after treatment with CA (0.2%, 0.4%, 0.6%, 0.8%), 0.4% HA, or normal control (NC). 
description: Representative images of GES-1 migration in the scratch wound healing assay at 0 h, 12 h, and 24 h after treatment with CA (0.2%, 0.4%, 0.6%, 0.8%), 0.4% HA, or normal control (NC).
DOI: 10.6075/j04x56pb
title: CIL:36537, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0c53kcp
title: CIL: 52388, 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: Tile x=4, y=5, z=6 from BL024199_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.15468/dl.m4vbfe
title: Occurrence Download

description: A dataset containing 893809 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Aetobatus ocellatus",
 "TaxonKey is Alopias vulpinus",
 "TaxonKey is Anoxypristis cuspidata",
 "TaxonKey is Carcharhinus albimarginatus",
 "TaxonKey is Carcharhinus amblyrhynchoides",
 "TaxonKey is Carcharhinus amblyrhynchos",
 "TaxonKey is Carcharhinus amboinensis",
 "TaxonKey is Carcharhinus brevipinna",
 "TaxonKey is Carcharhinus falciformis",
 "TaxonKey is Carcharhinus leucas",
 "TaxonKey is Carcharhinus limbatus",
 "TaxonKey is Carcharhinus longimanus",
 "TaxonKey is Carcharhinus macloti",
 "TaxonKey is Carcharhinus melanopterus",
 "TaxonKey is Carcharhinus plumbeus",
 "TaxonKey is Carcharhinus sorrah",
 "TaxonKey is Carcharodon carcharias",
 "TaxonKey is Chiloscyllium punctatum",
 "TaxonKey is Eucrossorhinus dasypogon",
 "TaxonKey is Eusphyra blochii",
 "TaxonKey is Galeocerdo cuvier",
 "TaxonKey is Glaucostegus typus",
 "TaxonKey is Gymnura australis",
 "TaxonKey is Hemipristis elongata",
 "TaxonKey is Hemiscyllium ocellatum",
 "TaxonKey is Hemiscyllium trispeculare",
 "TaxonKey is Himantura leoparda",
 "TaxonKey is Isurus oxyrinchus",
 "TaxonKey is Lamna nasus",
 "TaxonKey is Loxodon macrorhinus",
 "TaxonKey is Mobula alfredi",
 "TaxonKey is Mobula birostris",
 "TaxonKey is Mobula eregoodoo",
 "TaxonKey is Nebrius ferrugineus",
 "TaxonKey is Negaprion acutidens",
 "TaxonKey is Pastinachus ater",
 "TaxonKey is Pateobatis fai",
 "TaxonKey is Pateobatis jenkinsii",
 "TaxonKey is Prionace glauca",
 "TaxonKey is Pristis zijsron",
 "TaxonKey is Rhina ancylostoma",
 "TaxonKey is Rhizoprionodon acutus",
 "TaxonKey is Rhynchobatus australiae",
 "TaxonKey is Sphyrna lewini",
 "TaxonKey is Stegostoma tigrinus",
 "TaxonKey is Taeniura lymma",
 "TaxonKey is Taeniurops meyeni",
 "TaxonKey is Triaenodon obesus",
 "TaxonKey is Urogymnus asperrimus",
 "TaxonKey is Urogymnus granulatus"
 ]
 },
 "HasCoordinate is true",
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Material citation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Observation",
 "BasisOfRecord is Occurrence evidence",
 "BasisOfRecord is Specimen"
 ]
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 893809 records from 661 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009364-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0542mtb
title: CIL:1724, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 2 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0251hh3
title: CIL:40386, Psidium guajava. In Cell Image Library

description: Image collected on a Zeiss DSM 962 SEM. Complete specimen preparation protocol available at:
http://remf.dartmouth.edu:8080/EM-Wiki/36
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; shadowing and plating
Processing history: unprocessed raw data
description: Scanning electron microscope image of cross-section through a Psidium guajava stem. The image shows the thin outer epidermal layer with a thick layer of cortex beneath. The vascular area consists of a secondary phloem and primary xylem, with vascular cambium in between. The central pith has some mucilage present.This image is part of a group on botanical stems (CIL:40378-40395).
DOI: 10.6075/j0f18z9g
title: CIL: 52964, 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: Image 4, z=15 from SC_011
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0k93736
title: CIL: 53047, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Image 3, z=14 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
DOI: 10.6075/j0z31xrk
title: CIL:12080, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of microtubules that sometimes extend deep into the cytosol from the basal bodies. They serve to guide the trichocysts to their docking sites at the plasma membrane (see Plattner, Westphal and Tiggemann, J. Cell Biol. 92:368-377, 1982). Immunogold labeled for anti-b-tubulin detects the location of microtubules. TEM taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 7,900X.
description: Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements