cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0kp816r
title: CIL:6264, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6263.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0qn65v2
title: CIL:6554, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 50,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6555.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j02f7mfg
title: CIL:6553, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 30,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6552
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0r78d9q
title: CIL:6552, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 30,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6553.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0gq6wsc
title: CIL:6519, Danio rerio, Outer plexiform layer 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. The third image is a 15,000X TEM image of the bipolar and horizontal cells interdigitating in the OPL layer of the zebrafish retina. This image, the fourth in the series, is a higher magnification (60,000X) of the dense synaptic bar and synaptic vesicles. 

Synaptic vesicles (V) surround the dense bar (DB) in the synaptic ribbon complex in the outer plexiform layer of the larval zebrafish retina. 10 dpf Image collected on a JOEL 1230 at 80 kV using a Gatan 967 slow-scan, cooled CCD camera at x60,000. 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/j02806nt
title: CIL:6517, Danio rerio, Outer plexiform layer of retina, Outer nuclear layer of retina. In Cell Image Library

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
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 this image, the second image, which is a higher magnification TEM image of the plexiform layer and the outer nuclear layer of the zebrafish retina. The third image 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. 

TEM image of larval zebrafish retina showing outer nuclear layer (ONL) and outer plexiform layer (OPL). Image collected on a JOEL 1230 at 80 kV using a Gatan 967 slow-scan, cooled CCD camera. 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.
DOI: 10.6075/j0rx9b21
title: CIL:6273, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6256.
DOI: 10.6075/j0959gm7
title: CIL:6557, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6556.
DOI: 10.6075/j0qf8rz4
title: CIL:6271, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6259.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0rr1wv6
title: CIL:46074, 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 26682 - 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/j01j9891
title: CIL:46088, 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 26748 - 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/j08914gb
title: CIL:46061, 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 26668 - 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.