cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0st7ndr
title: CIL:49105, 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 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

The experiment consists of 375 microtiter plates. Each plate has 384 wells. 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 24685 - 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. 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 experiment consists of 375 plates in 384-well format, for a data set comprised of 988,994 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 approximately 5 million image files in 16-bit TIFF format.
DOI: 10.6075/j0sb44zr
title: CIL:1924, 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 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: 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/j07w6bdc
title: CIL:1917, 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 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/j0pk0fd8
title: CIL:1916, 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 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: 10.57903/uj/0hyhvu
title: IR-R intervals of participants attended in psychological training groups conducted face to face and onlinenterwały
title: IR-R uczestników grup treningu psychologicznego prowadzonego stacjonarnie i online

description: Dane pozyskane w ramach projektu badawczego "W jednym rytmie. Style przywiązania a synchronizacja fizjologiczna i behawioralna uczestników grupowego treningu psychologicznego prowadzonego stacjonarnie i online”. Projekt badawczy został sfinansowany ze środków Narodowego Centrum Nauki (2022/06/X/HS6/00621). W ramach badań zebrano dane dotyczące interwałów pomiędzy uderzeniami serca uczestników badania w poszczególnych grupach. Dane zawierają interwały z 4 grup, w każdej grupie dane zebrano od 4 uczestników oraz psychologa prowadzącego spotkania grupowe.
description: Data obtained as part of the research project "In one rhythm. Attachment styles and physiological and behavioral synchronization of participants of group psychological training conducted on-site and online. The research project was financed by the National Science Center (2022/06/X/HS6/00621). As part of the study, the intervals between heartbeats of each participants were collected. The data contains R-R intervals from 4 groups, including 4 participants and the psychologist who led the group meetings.
DOI: 10.6075/j06w999f
title: CIL:1927, 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 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: 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/j01835s1
title: CIL:1915, 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 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/j0sx6bxd
title: CIL:19129, Spiroplasma kunkelii, Zea mays, plant cell, prokaryotic cell. In Cell Image Library

description: Micrograph of a semi-thick (1-2 µm) section of an infected maize leaf, with silver-enhanced immunogold labeling, that shows dark staining of corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) aggregates in phloem tissue (asterisk). The section was counter stained with toluidine blue. CIL:12591, from the same image group, is an unlabeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. Additional related images from this contributor are available in the Library.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: bright-field microscopy
Imaging mode: widefield illumination
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: toluidine blue; gold
Data qualification: Processed
DOI: 10.6075/j0610z24
title: CIL:19127, Spiroplasma kunkelii, Zea mays, plant cell, prokaryotic cell. In Cell Image Library

description: Immuno-gold labeling of corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) in sieve elements and other phloem cells of infected maize leaves. CIL:12589, from the same image group, is an unlabeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. Additional images from the same contributors are available in the Library.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt; gold
Data qualification: Processed
description: Detailed methods: Tissue was processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Gold particles used in immunolabeling CSS were 10nm. Negatives were scanned later to generate these electronic files. Abbreviations: S = CSS,t = tip structure.
DOI: 10.6075/j09p30br
title: CIL:19124, Spiroplasma kunkelii, Zea mays, plant cell, prokaryotic cell. In Cell Image Library

description: Detailed methods: Tissue was processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. Abbreviations: n = nucleus, pa = parenchyma, ph = phloem, S = CSS, xy = xylem.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt
Data qualification: Processed
description: Electron micrograph of corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) in sieve elements and other phloem cells of infected maize leaves. CIL:12586, from the same image group, is an unlabeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. Additional images from this contributor are available in the Library.
DOI: 10.6075/j02b8xpp
title: CIL: 53516. 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: AGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j00r9nh1
title: CIL:6518, Danio rerio, Outer plexiform layer of retina, Bipolar cell of retina. In Cell Image Library

description: This study of the zebrafish eye is a series of four images taken at increasing magnifications. The first image is the SEM block face of the zebrafish eye. This is followed by a second image that is a higher magnification TEM image of the plexiform layer and the outer nuclear layer of the zebrafish retina. This image, the third image in the series, is a 15,000X TEM image of the bipolar and horizontal cells interdigitating in the OPL layer of the zebrafish retina. The fourth image in the series is a higher magnification (60,000X) of the dense synaptic bar and synaptic vesicles. 

Bipolar and horizontal cells (H) interdigitate in the outer plixiform layer (OPL) of the zebrafish retina. The presynaptic cone membrane contains an arciform density (arrowhead) and synaptic vesicles (V). Image collected on a JOEL 1230 at 80 kV using a Gatan 967 slow-scan, cooled CCD camera at 15,000X. 70 nm thick section. 

Microwave processing, osmium tetroxoxide/osmid procedure for enhancing membranes, and copper lead en bloc staining.
Procedure for specimen preparation available at http://www.stanford.edu/~redhair/JoAnn_Buchanan.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; heat fixed tissue; tissue in epoxy resin embedment
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; lead salt; copper salt
Processing history: unprocessed raw data
DOI: 10.6075/j0f18zvn
title: CIL:40148, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Tissue came from either mice genetically engineered to overexpress human alpha synuclein (mouse strain, C57BL/6-DBA/2, overexpress a mutant form of alpha synuclein (A53T), 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.
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: The hippocampal area CA1 of a transgenic mouse engineered to overexpress human alpha synuclein under the Thy1 promotor, 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.
DOI: 10.6075/j01v5dnr
title: CIL: 53421, Rhizosolenia setigera, Plankton. In Cell Image Library

description: Choanoflagellate
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
description: 128x128 segmented image from volumetric hologram
DOI: 10.6075/j0ng4q1t
title: CIL: 50906, Caenorhabditis elegans (roundworm, nematode), Intestine cells and Oocytes. In Cell Image Library

description: Wild type Caenorhabditis elegans (N2 background) were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of intestine cells and Oocytes and the black arrow indicates nuclear envelope budding events.
description: Worms were cultured onto normal growing medium plates spread with Escherichia coli (OP50 strain) and high pressure frozen in a Wohlwend Compact 3 machine, followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0gb2487
title: CIL: 54877. In Cell Image Library

description: ih-MSCs were cultured in a rotating wall vessel (RWV) bioreactor (RCCS-8DQ bioreactor (Synthecon, Houston, TX) fitted with 10 mL high aspect ratio vessels on custom-fabricated 120 ± 6.2 μm diameter gelMA microcarriers. For this purpose, approximately 110,000 gelMA microcarriers with a combined growth area of 50 cm2 and 5×104 cells (1000 cells/cm2) were incubated in 10 mL of CCM in the RWV bioreactor at 24 revolutions per minute. Half of the media was replaced with fresh CCM every 2 days. iH-MSCs fixed with 4% paraformaldehyde and fluorescently labeled with CellTracker Green (green), DRAQ-5 (blue), and DiI (gold) in the cytoplasm, nuclei, and plasma membrane, respectively. Label-free elastic scattering (white) and trasmitted light (grey) are also used to visualize the sample.

Passage 7 Day 3 single cell labeled with CelllTracker Green in the cytoplasm.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
description: The adoption of cell-based therapies into the clinic will require tremendous large-scale expansion to satisfy future demand, and bioreactor-microcarrier cultures are best suited to meet this challenge. A robust optical imaging and image-analysis assay to non-destructively quantify cell number and cell volume was developed using fluorescence and elastic scattering contrast. This assay was successfully applied to monitor cellular growth of induced pluripotent derived mesenchymal stem cells (iH-MSCs) attached to spherical hydrogel microcarriers over time. Elastic scattering and fluorescence lightsheet microscopy were used to quantify cell volume and cell number at varying spatial scales. The fluorescence-based assay is used as ground truth data to correlate the elastic scattering-based assay data.

Fig 2a,c Fixed passage 7 day 3 ih-MSC infiltrating the center of a microcarrier.
description: Imaging mode: Zeiss Z.1 Lightsheet microscope (fluorescence and scattering)
Visualization methods: FIJI/ImageJ