cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0p26xhh
title: CIL:45799, 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 24732 - 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.nsmnk3
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "OccurrenceStatus is Present",
 "TaxonKey is Tetracerus quadricornis"
 ]
}

 The dataset includes 44 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009673-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j00r9nsm
title: CIL:45772, 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 24352 - 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/j0cc0zr3
title: CIL:7666, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Higher resolution image of the surface of Nassula aurea. Early endosomes and clathrin coated vesicles. One clathrin coated pit at the bottom of a parasomal sac is shown. TEM taken on 2/22/71 by M. Aihara with Hitachi HU11A operating at 50kV. Neg. 10,750X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available 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.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0c24vds
title: CIL:7750, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A higher resolution cross section of the oral basket from Nassula aurea (C.N.R.S., Yvette, France) through its “waist”. Rods, rod lamellae, and the surrounding sheath are seen. Cytopharyngeal vesicles fill the basket lumen and are scattered outside the basket. TEM taken on 3/2/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 6,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available 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.

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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j05h7fbp
title: CIL:7663, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High resolution image of the detail of the three fibers supporting a basal body. A striated kinetodesmal fiber extends anteriorly from the basal body, a postciliary microtubular ribbon extends posteriorly and a transverse microtubular ribbon extends to the right of the anterior-posterior axis of the row of basal bodies. Basal bodies are composed of 9 triplet fibers each set at a tangent to the cylinder of the long axis of the bb. TEM taken on 3/4/69 by R. Allen with Philips 300 operating at 60kV. Neg. 39,900X. The raw film was scanned with an Epson Perfection V750 Pro. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j04j0d6v
title: CIL:7664, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution image of cytopharyngeal rods, composed of microtubular bundles, form the wall of the basket. Rod lamellae are attached to one side of each rod. TEM taken on 3/13/69 by R. Allen with Philips 300 operating at 60kV. Neg. 16,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available 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.

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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.15468/dl.ecnyjk
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Epipactis xanthophaea"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009675-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0cj8chp
title: CIL:7667, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High resolution of the detail of the cytopharyngeal basket from Nassula aurea. Microtubules make up the rods, rod lamellae and sheath. TEM taken on 3/2/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available 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.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0wq032w
title: CIL:770, Patiria miniata, sperm. In Cell Image Library

description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 3 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 160 (this image), 120, and 104eV.
description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: inelastic scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
DOI: 10.6075/j0445kpz
title: CIL:769, Patiria miniata, sperm. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: inelastic scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 3 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 170, 160, and 120eV (this image).
DOI: 10.6075/j0qr4wd6
title: CIL:768, Patiria miniata, sperm. In Cell Image Library

description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 3 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 170 (this image), 160, and 120eV.
description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: inelastic scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
DOI: 10.6075/j0c24vf7
title: CIL:7744, Potorous tridactylus tridactylus, primary cell line cell. In Cell Image Library

description: Preparation: cryofixed tissue; tissue in plastic embedment; freeze substitution
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); film
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: electron-dense stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Details of a cryofixed Ptk tissue culture cell showing Golgi apparatus, mitochondria and a segment of nucleus with nucleolus at right. 40 nm epon section prepared from plunge frozen,and freeze substituted specimen. Image recorded at 55,000x with a Philips CM10 TEM operated at 80KV.
DOI: 10.6075/j0416w93
title: CIL:774, Patiria miniata, sperm. In Cell Image Library

description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 3 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 160, 120, and 104eV (this image).
description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: inelastic scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
DOI: 10.6075/j0st7p4k
title: CIL:773, Patiria miniata, sperm. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: inelastic scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 3 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 160, 120 (this image), and 110eV.
DOI: 10.6075/j0d50m7g
title: CIL:772, Patiria miniata, sperm. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: inelastic scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 3 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 160, 120, and 104eV (this image).
DOI: 10.6075/j0df6qff
title: CIL:775, Patiria miniata, sperm. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: electron scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 4 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 160 (this image), 170, 120, and 110eV.