cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0ht2mxp
title: CIL:46255, 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 26166 - 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/j0t43rvq
title: CIL:11993, Drosophila melanogaster, epithelial cell. In Cell Image Library

description: TIRF time lapse of myosin-GFP in a cell with a symmetric monopolar spindle from metaphase to anaphase (cell was depleted of Klp61F [kinesin-5] and BubR1 by RNAi). At anaphase, myosin-GFP concentrates at the cell perimeter and becomes depleted from the central regions of the adhered cortex. Slowly, myosin breaks symmetry and ultimately relocalizes to the middle. This video corresponds to the image in Fig. 6 and video 10 from J Cell Bio 186:727-738, 2009.
Total internal reflection microscopy was performed using a microscope (Perfect-focus TE2000; Nikon) with a 100×, 1.45 NA objective (Nikon) and illumination from either a 488-nm argon laser (100 mW) or a 491-nm solid-state laser (100 mW) and a 561-nm solid-state laser (50 mW). For dual-color TIRF microscopy, we used a triplepass dichroic filter (z491/561/633rpc) and changed the emission filter (ET525/50 or ET595/50; both from Chroma Technology Corp.) with a filter wheel placed before the camera. In some cases, an excitation notch filter was used in the filter cube (NF01-405/488/561/635; Semrock, Inc.). Images were typically captured every 2-3 s with a 50-200ms exposure with an EM charge-coupled device camera (iXon; Andor Technology). The microscope was controlled and images were acquired using open source MicroManager software (http://www.micro-manager.org).
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: TIRF
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0qr4x7c
title: CIL:39661, 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: 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: 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
DOI: 10.6075/j0gt5mxh
title: CIL: 54557, Lilium longiflorum, reproductive cell (microsporocyte). In Cell Image Library

description: Metaphase II in a diploid lily. The chromosomes of both nuclei are lined up on the metaphase II plates.
description: Imaging mode: light micrograph
Visualization methods: DNA specific contrast staining using Feulgen staining
description: Feulgen stained light microscopy image collected using a bright field zeiss microscope, using a 100X, N.A. 1.4 Neuflar lens.
DOI: 10.6075/j07m07n7
title: CIL: 54196. In Cell Image Library

description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j028076d
title: CIL: 53324, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 24.3 degrees Celcius
description: 24.3 degrees ℃
DOI: 10.15468/dl.df7f2b
title: Occurrence Download

description: A dataset containing 20818 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acer pictum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "EventDate is greater than or equal to 1991-01-01",
 "EventDate is less than or equal to 2025-10-31"
 ]
}

 The dataset includes 20818 records from 140 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009379-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0ms3rnq
title: CIL:41736, Bacillus subtilis. In Cell Image Library

description: A confocal micrograph showing Bacillus subtilis, a Gram-positive, rod-shaped bacterium that is commonly found in soil. Distinct lineages of bacteria expressing different fluorescent proteins were initially mixed randomly on a petri dish. As the bacteria grow, they organize themselves into reproducible patterns and shapes that can be predicted with mathematical models.This image is part of a synthetic biology project involved in designing artificial genetic circuits for pattern formation in bacterial colonies and plant tissues. The horizontal field width of this image is 500 microns. Wellcome Image Award 2012.
description: B0008257. 2011 Collection: Wellcome Images Copyrighted work available under Creative Commons by-nc-nd 2.0 UK: England & Wales, see http://images.wellcome.ac.uk/indexplus/page/Prices.html
description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: TagRFP-T; mTagBFP; mKate2FP; mOrange2FP; sfGFP
DOI: 10.6075/j0mg7nf6
title: CIL:25696, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Time lapse series of cell growth and division in cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) using differential interference contrast optics. This time series is grouped in the Cell Image Library with a corresponding movie.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
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: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica HCX PLAN APO 100x NA 1.35 DIC objective lens. images were captured at 3 second intervals with a Hamamatsu ORCA-ER2 CCD camera using Simple PCI 6.6.0.0 software.
DOI: 10.6075/j0dv1j2p
title: CIL:21992, Didinium nasutum, Paramecium sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: chemically fixed tissue; lyophilized specimen; Parducz fixative; Au/Pd metal sputter-coat
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: illumination by electrons; secondary_electron imaging
Parameter imaged: illumination by electrons; secondary electron generation; secondary_electron imaging
Source of contrast: detection of electrons
Visualization methods: shadowing and plating
Processing history: recorded image; film
Data qualification: Raw
description: Didinium ingests Paramecium. Note that Paramecium is nearly the waiting food vacuole and the proboscis of Didinium is beginning to reform. This micrograph also shows the metachronous waves of cilia in the two characteristic ciliary girdles of Didinium nasutum and bacteria on the surface that may represent ectosymbionts. The micrograph was taken in 1968 by G. Antipa on a Cambridge Mark IIA operating at 20kV. The negative magnification is 630X. Further details are available at Wessenberg, H. and Antipa, G. 1970. Capture and ingestion of Paramecium by Didinium nasutum. J. Protozool. 17:250-270.
DOI: 10.6075/j0kh0mmd
title: CIL:258, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Thin section electron microscopy of diaphragm (skeletal) muscle from a wild type mouse.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 30,000X magnification.

This image is part of a set of wild type diaphragm muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide 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: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
DOI: 10.6075/j0833rhx
title: CIL: 51818, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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: ~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: 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/j0nk3d3n
title: CIL:2795, 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: 10.6075/j02b8xjw
title: CIL: 52279, 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=4, y=1, z=2 from BL_024216_Myc_Terc
DOI: 10.6075/j0j67g4q
title: CIL:1156, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 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.
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.
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
DOI: 10.6075/j0mp525w
title: CIL:25373, 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 (arrows) buds through nuclear membranes and accumulates in perinuclear space in cells of the nerve ganglia. Abbreviations: N, nucleus. The accompanying image in this image group is unlabeled. 
 
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: recorded image
Data qualification: Processed
DOI: 10.6075/j0513x4f
title: CIL:25401, Drosophila melanogaster, fat body cell. In Cell Image Library

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: Whole mount squash of Drosophila polytene chromosome viewed with high voltage EM showing a series of bands and interbands. This micrograph was recorded with a tilt angle of 56 degrees. The accompanying grouped image, taken at 45 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Fat cells 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/j0sb44qm
title: CIL:25400, Drosophila melanogaster, salivary gland cell. In Cell Image Library

description: Whole mount squash of Drosophila polytene chromosome viewed with high voltage EM showing a series of bands and interbands. This micrograph was recorded 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
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: 10.34740/kaggle/dsv/13564917
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.17490824
title: Genome of the Predatory Volute Melo melo
DOI: 10.5281/zenodo.17490825
title: Genome of the Predatory Volute Melo melo