cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j04t6hbx
title: CIL:7334, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the contractile vacuole in diastole (filling phase). Decorated spongiome surrounds the CV. The macronucleus, micronucleus, cytopharynx, and basal bodies of perioral membranelle are included. TEM taken on 6/10/69 by R. Allen with Philips 300 operating at 60kV. Neg. 11,800X. The raw film was scanned with a Nikon Coolscan 9000ED. This image is suitable 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/).
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
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j06t0kmp
title: CIL:7333, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Image of the scopula, the stalk forming region at the aboral end of the cell body of Opercularia coarctata. A group of basal bodies each gives rise to a modified cilium that gives rise to a cylinder of striated fibrous 'straws' that occupy the lumen of the non-contractile stalk. This image shows a basal body of the trochal region, the end of the empty nascent food vacuole tube that is surrounded by lamellar microtubules that arise from the cytopharynx, the macronucleus, myonemes, and a perioral kinetid.
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;intensitiesquantitation
description: TEM taken on 6/10/69 by R. Allen with Philips 300 operating at 60kV. Neg. 11,800X. Bar = 1.0µm. 
 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/j06972kh
title: CIL:7329, Mus musculus, blood vessel endothelial cell, primary cell line cell. In Cell Image Library

description: Primary endothelial cells from transgenic mouse expressing myosin heavy chain 2A fused to mCherry (red), transfected with GFP-myosin (green) regulatory light chain expression vector and demonstrate the role of myosin in cell division. Cells are embedded in 3D collagen gels. mage Name: myosin cell division timelapse
Biological Source: Primary mouse (mus musculus) aortic endothelial cell. 
2D images over time. 0.1274 micron/pixel, 520x490 pixels, 20 seconds interval between timepoints.Time shown is in minutes:seconds. Images collected with a spinning disk confocal on a Nikon TE1000 with a 60X 1.2NA water objective using 400 ms exposure for mCherry and 200 ms for GFP.
See Fischer et al for details regarding preparation. http://www.ncbi.nlm.nih.gov/pubmed/19185493
description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro; cells in 3D matrix
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; mCherryFP
Processing history: unprocessed raw data
DOI: 10.6075/j0wd3zk0
title: CIL:7328, Dictyostelium discoideum, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: A movie of phagosome neutralization visualized using FITC-yeast. Amoebae of Dictyostelium discoideum were fed living budding yeast (S. cerevisiae strain TH2-1B) that had been labeled with fluorescein isothiocyanate (FITC, 0.25 mg/ml). The amoebae in phosphate buffer (pH 6.4) were examined 1 ½ hours later using a Zeiss LSM510 laser scanning confocal microscope; frames were collected in a single focal plane at 5-second intervals. The yeast fluoresce brightly in the extracellular medium, but are dim in acidic phagosomes because FITC fluorescence is quenched at acidic pH. At the end of the endocytic pathway, a phagosome is neutralized prior to exocytosis of the indigestible yeast carcass; that process is visualized here. The amoebae are also expressing two other fluorescent markers that are barely visible, mRFP-LimE-delta, which labels actin filaments, and VatM-GFP, a subunit of the V-ATPase. Three hundred frames from the time series were exported as .tif images (available at CIL:7327)and saved as a stack in ImageJ; they are also shown as a movie (.avi) at 10fps. For related experiments and further details, see Clarke et al., PLoS ONE 5:e8585 (2010).
description: Preparation: whole mounted tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy; fluoresence quenching
Imaging mode: recorded image; single-spot confocal microscopy
Parameter imaged: single-spot confocal microscopy
Source of contrast: fluorescence microscopy
Visualization methods: Fluorescein (FITC); PA-mRFP; PA-GFP
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j09s1q24
title: CIL:7327, Dictyostelium discoideum, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: Phagosome neutralization visualized using FITC-yeast. Amoebae of Dictyostelium discoideum were fed living budding yeast (S. cerevisiae strain TH2-1B) that had been labeled with fluorescein isothiocyanate (FITC, 0.25 mg/ml). The amoebae in phosphate buffer (pH 6.4) were examined 1 ½ hours later using a Zeiss LSM510 laser scanning confocal microscope; frames were collected in a single focal plane at 5-second intervals. The yeast fluoresce brightly in the extracellular medium, but are dim in acidic phagosomes because FITC fluorescence is quenched at acidic pH. At the end of the endocytic pathway, a phagosome is neutralized prior to exocytosis of the indigestible yeast carcass; that process is visualized here. The amoebae are also expressing two other fluorescent markers that are barely visible, mRFP-LimE-delta, which labels actin filaments, and VatM-GFP, a subunit of the V-ATPase. Three hundred frames from the time series were exported as .tif images and saved as a stack in ImageJ; they are also shown as a movie (.avi) at 10fps (available at CIL:7328). For related experiments and further details, see Clarke et al., PLoS ONE 5:e8585 (2010).
description: Preparation: whole mounted tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy; fluoresence quenching
Imaging mode: recorded image; single-spot confocal microscopy
Parameter imaged: single-spot confocal microscopy
Source of contrast: fluorescence microscopy
Visualization methods: Fluorescein (FITC); PA-mRFP; PA-GFP
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j04j0d3h
title: CIL:7326, Dictyostelium discoideum, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: Preparation: whole mounted tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy; fluoresence quenching
Imaging mode: recorded image; single-spot confocal microscopy
Parameter imaged: single-spot confocal microscopy
Source of contrast: fluorescence microscopy
Visualization methods: Fluorescein (FITC); PA-mRFP; PA-GFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: A movie that shows phagosome acidification and neutralization visualized using FITC-yeast. Amoebae of Dictyostelium discoideum were fed living budding yeast (S. cerevisiae strain TH2-1B) that had been labeled with fluorescein isothiocyanate (FITC, 0.25 mg/ml). The amoebae in phosphate buffer (pH 6.4) were examined 1 ½ hours later using a Zeiss LSM510 laser scanning confocal microscope; frames were collected in a single focal plane at 5-second intervals. The yeast fluoresce brightly in the extracellular medium, but are dim in acidic phagosomes because FITC fluorescence is quenched at acidic pH. At the end of the endocytic pathway, phagosomes are neutralized and the indigestible yeast carcass is exocytosed. This time series shows fluctuations in fluorescence intensity just prior to exocytosis of a yeast. That yeast is promptly phagocytosed by another cell, and the yeast grows dim as the phagosome is acidified. Meanwhile a second yeast in the same cell grows brighter, presumably in preparation for exocytosis. The amoebae are also expressing two other fluorescent markers, which are faintly visible, mRFP-LimE-delta, which labels actin filaments, and VatM-GFP, a subunit of the V-ATPase. Three hundred frames from the time series were exported as .tif images and saved as a stack in ImageJ (and available at CIL:7625); they are shown here as a movie (.avi) at 10fps. For related experiments and further details, see Clarke et al., PLoS ONE 5:e8585 (2010).
DOI: 10.6075/j07943rb
title: CIL:7325, Dictyostelium discoideum, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: Phagosome acidification and neutralization visualized using FITC-yeast. Amoebae of Dictyostelium discoideum were fed living budding yeast (S. cerevisiae strain TH2-1B) that had been labeled with fluorescein isothiocyanate (FITC, 0.25 mg/ml). The amoebae in phosphate buffer (pH 6.4) were examined 1 ½ hours later using a Zeiss LSM510 laser scanning confocal microscope; frames were collected in a single focal plane at 5-second intervals. The yeast fluoresce brightly in the extracellular medium, but are dim in acidic phagosomes because FITC fluorescence is quenched at acidic pH. At the end of the endocytic pathway, phagosomes are neutralized and the indigestible yeast carcass is exocytosed. This time series shows fluctuations in fluorescence intensity just prior to exocytosis of a yeast. That yeast is promptly phagocytosed by another cell, and the yeast grows dim as the phagosome is acidified. Meanwhile a second yeast in the same cell grows brighter, presumably in preparation for exocytosis. The amoebae are also expressing two other fluorescent markers, which are faintly visible, mRFP-LimE-delta, which labels actin filaments, and VatM-GFP, a subunit of the V-ATPase. Three hundred frames from the time series were exported as .tif images and saved as a stack in ImageJ; they are also shown as a movie (.avi) at 10fps (available at CIL:7326). For related experiments and further details, see Clarke et al., PLoS ONE 5:e8585 (2010).
description: Preparation: whole mounted tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy; fluoresence quenching
Imaging mode: recorded image; single-spot confocal microscopy
Parameter imaged: single-spot confocal microscopy
Source of contrast: fluorescence microscopy
Visualization methods: Fluorescein (FITC); PA-mRFP; PA-GFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j03r0rwq
title: CIL:7321, Escherichia coli, prokaryotic cell. In Cell Image Library

description: This is one of four related images of F-pili (conjugative pili encoded by the F plasmid of E. coli) dynamics by live-cell imaging. There are 2 movie (.avi) files and 2 files (.tiff) from the movies. The movies show that F-pili normally undergo cycles of extension and retraction in the absence of any obvious triggering event such as contact with a recipient cell.

Retraction of an F-pilus. E. coli strain HfrH expressing the red fluorescent marker DsRed Express were mixed with R17 bacteriophage labeled with Alexa 488 (green); R17 bacteriophage (NCBITaxon:12026) bind to the sides of F-pili. 

Samples were imaged by using a Zeiss LSM 510 confocal microscope with a Plan-Apochromat 63 × 1.4 N.A. DIC objective. Alexa-488 was excited with the 488-nm line of an argon laser with a 505–530-nm filter for emission, and DsRed was excited with the 543-nm line of a HeNe laser, with a 560-nm long pass filter for emission. An HFT UV/488/543 beam splitter was used. Images were collected in a single focal plane at 2 s intervals and accompanying movies (.avi) are playing at 10fps.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: DsRed-ExpressFP; Alexa Fluor 488; macromolecular probe
Processing history: unprocessed raw data
DOI: 10.6075/j07p8xd3
title: CIL:7322, Escherichia coli, prokaryotic cell. In Cell Image Library

description: This is one of four related images of F-pili (conjugative pili encoded by the F plasmid of E. coli) dynamics by live-cell imaging. There are 2 movie (.avi) files and 2 files (.tiff) from the movies. The movies show that F-pili normally undergo cycles of extension and retraction in the absence of any obvious triggering event such as contact with a recipient cell.

Retraction of an F-pilus. E. coli strain HfrH expressing the red fluorescent marker DsRed Express were mixed with R17 bacteriophage labeled with Alexa 488 (green); R17 bacteriophage (NCBITaxon:12026) bind to the sides of F-pili. 

Samples were imaged by using a Zeiss LSM 510 confocal microscope with a Plan-Apochromat 63 × 1.4 N.A. DIC objective. Alexa-488 was excited with the 488-nm line of an argon laser with a 505–530-nm filter for emission, and DsRed was excited with the 543-nm line of a HeNe laser, with a 560-nm long pass filter for emission. An HFT UV/488/543 beam splitter was used. Images were collected in a single focal plane at 2 s intervals and accompanying movies (.avi) are playing at 10fps.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: DsRed-ExpressFP; Alexa Fluor 488; macromolecular probe
Processing history: unprocessed raw data
DOI: 10.6075/j0qc03j5
title: CIL:7313, Didinium nasutum, 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: elastic scattering
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: A high resolution, longitudinal section through one toxicyst and one bundle of microtubules (nematodesma) of the oral area of Didinium involved in the killing and ingesting of large prey. Didinium specializes in consuming Paramecium, an organism nearly their own size in less than one minute at standard room temperature. This slightly oblique longitudinal section allows the opportunity to visualize the longitudinal substructure of the hexagonally packed microtubules that support the cytopharynx and assistin the process. TEM taken on 5/20/69 by R. Allen with Philips 300 operating at 60kV. Neg. 6,370X. The raw film was scanned with a Nikon Coolscan 9000ED. This image is suitable 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/j0z899zk
title: CIL:46280. In Cell Image Library

description: Plate 25707 - 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.
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.
DOI: 10.6075/j0qc023x
title: CIL:46275, Homo sapiens. In Cell Image Library

description: Plate 25855 - 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.
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.