cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0tx3d26
title: CIL:35161, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Hoechst 33258; DiOC6 (3,3'-dihexyloxacarbocyanine iodide)
description: Live mitotic HeLa cell treated with control siRNA, DiOC6(3)to label mitotic membranes (green), and Hoechst 33258 to label chromosomes (blue). Confocal images were taken at 0.118 μm steps along the Z-axis.
description: A Leica TCS SP5 DM6000B confocal laser scanning microscope with HCX Plan Apo 63x/1.4 oil objective lens was used to capture the images.
DOI: 10.6075/j0gb23qn
title: CIL: 53751, Homo sapiens, HeLa. In Cell Image Library

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.
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/j0b56j4z
title: CIL:45797, 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 24726 - 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: 10.6075/j08051gh
title: CIL:40418, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Transmission electron micrograph showing an organelle in the process of circularizing from a BY4716 wildtype cell treated with 60¬µM sertraline. (40,000X).This image is part of an image group of cisternae images, CIL: 40417-40423. The contributor of these images encourages comments regarding whether these structures are Golgi or immature autophagosomes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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: osmium tetroxide
Processing history: unprocessed raw data
description: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
DOI: 10.6075/j0cj8crt
title: CIL:1931, 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 4 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/j02r3qbz
title: CIL:37220, Rattus, non-myelinating Schwann cell. In Cell Image Library

description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification x63,000.
description: Electron micrograph of an unmyelinated nerve Schwann cell from a rat tongue. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: chemically fixed tissue
Relation to intact cell: microtome-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: osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0cn735j
title: CIL:1765, 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 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
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.
DOI: 10.6075/j0057fhx
title: CIL: 52919, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
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 11, z=12 from SC_007
DOI: 10.6075/j0sf2w5t
title: CIL:39652, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0qn663m
title: CIL:39358, Zea mays. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: uranyl salt; shadowing and plating
Processing history: unprocessed raw data
description: Scanning electron microscope image of corn leaf surface.
description: Instrument: FEI XL-30 FEG ESEM. Technical protocol available at http://remf.dartmouth.edu:8080/EM-Wiki/36
DOI: 10.6075/j0pz583v
title: CIL:1695, Caenorhabditis elegans. In Cell Image Library

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: 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.
DOI: 10.6075/j0gm8649
title: CIL:10951, blood vessel endothelial cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed 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
Visualization methods: electron-dense stain
Data qualification: Processed
description: Two electron micrographs of smooth muscle cells in a small artery, surrounded by a light gray zone of interspaces composed of an elastic fiber and collagen-rich basement membrane. The elastica interna is a lamina composed of elastin fibers, and enables arteries to stretch. Figures 27 (upper) and 28 (lower) from Chapter 1 (The Cell Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.5281/zenodo.10688436
title: Extent of threats to marine fish from the online aquarium trade in the United States
DOI: 10.6075/j0db80z6
title: CIL:13105, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of the cross section through a radial arm of the contractile vacuole complex. The collecting canal occupies the center of the arm whose membrane is supported by the radial microtubular ribbon which has now divided into at least six segments and surrounds the canal. Gaps between the segments are where the mass of membrane tubules of the smooth spongiome opens into the canal. Decorated tubules occurring in bundles form the peripheral layer of the radial arm. TEM taken on 5/2/79 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 18,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. 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/).
DOI: 10.6075/j09k49c8
title: CIL:12340, 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; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol, and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. There is a high resolution version of this image in the library (CIL:39114) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: A view of the cytopharynx and its nascent food vacuole forming region. The flattened pharyngeal vesicles that may contain monolayers or bilayers of lipids seem to be equivalent to the discoidal vesicles of Paramecium that provide membrane for food vacuole growth. They approach and fuse with the cytopharyngeal membrane between the lamellae (cytopharyngeal ribbons). TEM taken on 7/29/67 by R. Allen with Philips 200 operating at 60kV. Neg. 9,000X. Bar = 0.5µm.
DOI: 10.6075/j0zs2vp4
title: CIL:24778, Rattus norvegicus, epithelial cell. In Cell Image Library

description: This image is one from a set of 40nm thick serial sections through part of a Golgi ribbon from a normal rat kidney cell, generated using transmission electron microscopy following incubation at 15°C to block transport out of the Golgi complex. Following temperature block, large bulging domains appear on the three trans-most cisternae. The images in this set were used in 3-dimensional reconstructions of the Golgi apparatus. For more information see: Ladinsky et al. (2002) Structure of the Golgi and distribution of reporter molecules at 20°C reveals the complexity of the exit compartments, Mol Biol Cell 13:2810-2825. The other images from this serial set are included in this image group.
description: Cells were grown on 100-mesh gold EM grids, and maintained at 15°C for 4 hours before plunge freezing in liquid nitrogen (BalTec HPM-010), followed by freeze-substitution (1% glutaraldehyde, 0.1% tannic acid in acetone, replaced with 4% osmium tetroxide and 0.01% uranyl acetate), then embedded in Epon-Araldite and sectioned at 40nm (UltraCut-UCT, Leica). Sections were transferred to formvar-coated copper-rhodium slot grids (EMS) and stained with 2% aqueous uranyl acetate and Reynold's lead citrate. Images were acquired at a magnification of 13,000X with an FEI Tecnai TF20 transmission EM. For additional details refer to: Mol Biol Cell 13:2810-2825.
description: Preparation: tissue in epoxy resin embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed 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
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0mk6d21
title: CIL:40138, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: The cerebral cortex of a non-transgenic mouse immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
DOI: 10.15468/dl.qtjxj9
title: Occurrence Download

description: A dataset containing 665 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fedia cornucopiae",
 "Country is Portugal",
 "HasCoordinate is true"
 ]
}

 The dataset includes 665 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011597-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.em4ft4
title: Occurrence Download

description: A dataset containing 370 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriopsis Lindl."
 ]
}

 The dataset includes 370 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006707-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hvxab7
title: Occurrence Download

description: A dataset containing 84855 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Thalurania glaucopis"
 ]
}

 The dataset includes 84855 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001402-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eu6jfm
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Struthioniformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((30 -90,60 -90,60 -60,30 -60,30 -90))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001469-251009101135966/datasets/export for details.