cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0rj4h1z
title: CIL:46075, 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 26683 - 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.tve3kb
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Hong Kong, Macao, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cynomorium songaricum"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009420-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j03b6077
title: CIL:35808, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged MCM1. 
 
 MCM1 is a transcription factor involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes
 
These phase,gfp images are part of an image group that ranges from CIL:35880-35899. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
DOI: 10.6075/j0x92929
title: CIL:23047, Rattus, fibroblast. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; tannic acid
Relation to intact cell: platinum replica
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: uranyl salt; shadowing and plating; primary antibody plus labeled secondary antibody; immunogold
Processing history: unprocessed raw data
description: Association of plectin with MTs. Electron microscopy
of gelsolin-treated REF-52 cells after immunogold (10 nm) labeling for plectin. Plectin forms bridges between microtubules and intermediate filaments. Electron microscopy of cytoskeletons was performed as described (Svitkina et al., 1995). Briefly, cells on coverslips were lysed as for light microscopy, treated, with recombinant gelsolin NHz-terminal domain, fixed with glutaraldehyde, tannic acid and uranyl acetate, critical point dried, and coated with platinum and carbon. Image corresponds to Fig 5a from J Cell Biol. 1996 Nov;135(4):991-1007.
DOI: 10.6075/j0kh0nb7
title: CIL:841, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Visualization methods: Cyan fluorescent proteins from Aequorea
Processing history: unprocessed raw data
description: CFP-expressing neuron, 14 days in vitro. By two weeks, cultured hippocampal neurons have developed a morphology typical of mature neurons with an extensive axonal arbor, a tapered and branched dendritic arbor, and synaptic connections. Growth cones can be seen at the tips of axonal branches, and the dendritic arbor is studded with spines, specialized structures commonly associated with excitatory synapses. This image accompanies the second file in this image group combines the fluorescent and phase micrographs from the same field of view. Detailed methods: Embryonic rat hippocampal neurons were prepared and transfected with soluble CFP (excitation, 439; emission, 476) at plating (Dotap, Roche) as previously described (Kaech and Banker, 2006, Nat Protoc), fixed for 15 minutes (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4, warmed to 37°C, permeabilized with 0.25% Triton X-100 for 7 minutes, and rinsed with phosphate buffered saline at 14 days in vitro (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Images were acquired with a Leica DMRXA microscope with a mercury arc lamp, a 16X PL Fluotar (0.5 NA) oil immersion lens, Princeton Instruments Micromax CCD camera and MetaMorph software, using a Leica CFP filter cube. Linked images show: A) CFP expression throughout the extent of the neuron; B) a merged image of the fluorescent cell with respect to the phase image, generated with the MetaMorph overlay function.
DOI: 10.6075/j0xp73k7
title: CIL:12633, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: A high resolution of a quick-freeze deep-etch rotary shadowed replica of a parasomal sac from which a clathrin-coated preendosomal vesicle has pinched off. The typical clathrin cage structure is preserved. Fractured trichocyst at the lower left. TEM taken on 6/7/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 31,500X. Adapted with permission from the J. Cell Sci. 101:449-461, 1992. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0k35tq0
title: CIL:39620, Saccharomyces cerevisiae. In Cell Image Library

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.
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.
DOI: 10.6075/j0697326
title: CIL: 52199, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
DOI: 10.6075/j0rj4jm0
title: CIL:40257, Rattus norvegicus, peripheral neuron. In Cell Image Library

description: Chemical fixation with 2% paraformaldehyde and 2.5% glutaraldehyde via vascular perfusion in 0.15M cacodylate buffer (pH 7.4) at 37 degrees C 

Neuronal sections cut to a thickness of 300-500 nm were taken on 100 mesh copper clamshell grids. The sections on the grid were stained for 30 minutes to 60 minutes in 2% aqueous uranyl acetate then approximately 15 min in lead salts. 20nm fiducial markers were placed on the specimen.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: A single image from animation of the computed slices through a tomographic volume of mitochondria at the Node of Ranvier in rat peripheral nerve root. 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: Perkins et al. Mitochondrial configurations in peripheral nerve suggest differential ATP production. J. Struct. Biol. (2010), doi:10.1016/j.jsb.2010.06.017 http://www.ncbi.nlm.nih.gov/pubmed/20600951
DOI: 10.6075/j0fn14v8
title: CIL:37261, Bos taurus. In Cell Image Library

description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification x2,000.
description: Zymogen granule fraction Calf. This study demonstrated directly that the enzyme and proenzyme composition of proteins in pancreatic juice collected from an indwelling catheter in the bovine pancreatic duct correlated exactly with the protein composition obtained from lysed purified bovine zymogen granules. Subsequent studies showed that pancreatic digestive enzymes and proenzymes were secreted from the pancreas in parallel. In other words, each granule must contain, on average, the same composition of secretory proteins. This hypothesis was later directly tested by immuno-EM localization of trypsinogen and other secretory proteins in all zymogen granules in the bovine pancreas.
 Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: osmium tetroxide fixed tissue; n-butyl methacrylate embedded 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: lead salt
Processing history: scanned negative
DOI: 10.6075/j0rf5v3b
title: CIL:35770, Saccharomyces cerevisiae. In Cell Image Library

description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please read the microscopy section of the referenced paper for details before image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Clb2. Clb 2 is a cyclin-dependent protein kinase regulator, involving in G2/M transition of mitotic cell cycle and positively regulating spindle pole body separation. These phase and GFP images are part of an image group containing CIL 35760-35779. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j01c1w7t
title: CIL:41615, Cricetulus griseus, epithelial cell, ovary. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: squash preparation
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High Voltage Transmission EM of whole mitotic metaphase chromosomes from Chinese hamster ovary cells. This image was recorded at a specimen tilt of 54 degrees and is grouped with one taken at 46 degrees, creating a stereo pair giving an oblique 3D view of the chromosomes.
description: CHO cells arrested at metaphase with colcemid were treated with 67% D2O, in 0.07M phosphate buffer and squashed in 50% acetic acid. Preparations were transferred to EM grids and examined with the Wisconsin HVEM operated at 1MeV.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
DOI: 10.6075/j0rr1xzz
title: CIL: 54344, 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: Visualization methods: confocal microscopy
description: CAMK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.6075/j0m04586
title: CIL: 54732, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Cells imaged with bright field.
description: Live cell imaging.
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: bright field imaging
DOI: 10.6075/j0qz28mr
title: CIL:35203, Fundulus heteroclitus, epithelial cell. In Cell Image Library

description: Visualizations taken from intact embryos, injected with GFP-actin plasmid at 1-cell stage. Filmed during gastrulation.
description: This video shows the dynamics of the apical cell surface of individual cells of the enveloping layer in a killifish embryo. The fluorescent actin is seen to polymerize and depolymerize in cyclic waves that extend and retract these surface protrusions. Two neighboring cells from a continuous epithelium are expressing the fluorescent GFP-actin. The expression of this inserted gene is mosaic, with some cells expressing, and others not.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0gf0sfm
title: CIL:25512, Drosophila melanogaster, salivary gland. In Cell Image Library

description: Whole mount squash of polytene chromosomes from Drosophila salivary gland. Low magnification survey image of a cluster of chromosomes showing a series of bands and interbands was taken with a High Voltage EM.
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
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.
DOI: 10.6075/j0n878qg
title: CIL:35282, Rattus rattus, hepatocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Rhodamine; primary antibody plus labeled secondary antibody
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
description: Image was collected with 1 60X, 63X, or 100X oil immersion objective with a numerical aperture of 1.25 such that each pixel size was 0.23 X 0.23 um. The image was collected as part of a Z series with step size of 0.53 um. A Photometrics cooled CCD camera based on the KAF1400 chip was used.
description: Primary rat hepatocytes in culture fixed and stained for beta-tubulin. The microtubules form a network throughout the cytoplasm. In this image they are seen originating from a brighter and denser region adjacent to the cell nucleus.
 
 This is a single optical section where the cell meets the substrate collected by widefield fluorescence microscopy with a Photometrics camera with a KAF1400 chip. The imaging was performed at a microscopy course at Woods Hole Oceanographic Institute in October 1993 and deconvolved on VayTec software running on a Macintosh computer. At the time, deconvolution was new and novel for use by biologists.