cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0sq8znz
title: CIL:763, Patiria miniata, sperm. In Cell Image Library

description: Upon electron bombardment, some elements, such as P, show an electron energy loss profile with a peak at a specific energy loss value. By collecting a series of images of a field at different energy losses, it is possible to compute the relative amount of the element at each pixel and map the element's distribution, a technique known as electron spectroscopic imaging (ESI) or electron filtered transmission EM (EFTEM).
The 4 images in this group were recorded from unstained &lt;30 nm section with 5eV energy windows centered on 120, 104, 160 and 170 eV respectively using a Zeiss 902 energy filtered EM, making it possible to map the distribution of phosphorus (energy loss edge 160 eV) within the chromatin fibers. This image was recorded at 1o4 eV.
description: Preparation: glutaraldehyde fixed tissue; freeze substitution in Lowicryl
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: microscopy with lenses; transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: electron scattering
Visualization methods: electron energy loss window
Processing history: unprocessed raw data
DOI: 10.6075/j0tq60jk
title: CIL:7624, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of Nassula sp. showing rows of cross-sectioned basal bodies at the cell surface. TEM taken on 3/4/69 by R. Allen with Philips 300 operating at 60kV. Neg. 16,000X. 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
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: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j08c9v82
title: CIL:7590, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of Halteria fixed in cacodylate-buffered fixative and stained. The round, dark bodies, possibly pigment granules, which were transparent in other preparations are electron-opaque following this protocol. The alveoli are flattened and inconspicuous. There is little evidence of an epiplasm. TEM taken on 11/8/68 by R. Allen with Philips 300 operating at 60kV. Neg. 12,500X. 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0w094z4
title: CIL:7601, Halteria grandinella, 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 DNA replication band in macronucleus of Halteria. Like hypotrichs the macronucleus of this oligotrich has a DNA replication band where DNA is synthesized. The nucleolus is evident. TEM taken on 3/9/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 13,750X. 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/j0vq320d
title: CIL:759, 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, 160 (this image), 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: 10.15468/dl.qebakk
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Solanum melongena"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009204-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0mk6c6d
title: CIL:757, 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.
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 170, 160, 118 (this image), 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: electron energy loss
Visualization methods: EELs window
Processing history: unprocessed raw data
DOI: 10.6075/j0mk6bnt
title: CIL:7623, Rattus rattus, epithelial cell, rat kidney proximal tubule epithelial cell. In Cell Image Library

description: In this experiment, hemoglobin was used
as a mass tracer. The rat received two injections, each of 1 gm of 2 X crystallized bovine hemoglobin in ~5 ml saline, administered intraperitoneally, the first at 24 and the last at 16 hours before collecting kidney specimens. Fixative was perfused into the aorta of the rat (2% osmium tetroxide buffered at pH 7.6 with acetate-veronal). Tissue blocks were stained by placing them for 30 minutes in 1 per cent phosphotungstic acid in absolute ethanol prior to infiltration and were embedded in Epon. Thin sections were stained with lead hydroxide. Micrograph was taken at original magnification of 50,000 X with a Siemens Elmiskop I, operating at 60 or 80 kv, with a double condenser, and a 50 µ objective aperture. Digitization process: conversion from a 1200 dpi tiff, 3832 x 3260 pixels. Original image created on June 11, 1962. Original resource provided as a 3.25 x 4 inch lantern slide. Research conducted at The Rockefeller Institute of Medical Research (New York, NY).
description: Portion of a proximal convoluted tubule from a rat kidney with experimental hemoglobinuria. A mass of dense hemoglobin completely fills the tubule lumen and outlines the microvilli (MV) of the brush border. The penetration of hemoglobin along the intercellular spaces is blocked at the level of the tight junctions (also known as zonula occludens, ZO) and does not appear in the adherens junctions (zonula adherens, ZA) or in the distended intercellular spaces (IS) below the level of the shallow tight junctions. Hemoglobin also has been internalized via large clathrin coated vesicles (CV) and appears in endosomes (end) and lysosomes (lys). First demonstration that the tight junction acts as a barrier preventing passage of proteins along the intercellular spaces by forming a seal between adjacent cells. First demonstration of the shallow nature of the tight junctions between epithelial cells in the proximal tubule. Identical unlabeled image available as CIL# 7622. Image published as Figure 24 in Farquhar and Palade, 1963.
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: lead salt; phosphotungstic acid
Processing history: digitized lantern slide
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0rr1wzj
title: CIL:7622, Rattus rattus, epithelial cell, rat kidney proximal tubule epithelial cell. In Cell Image Library

description: Portion of a proximal convoluted tubule from a rat kidney with experimental hemoglobinuria. A mass of dense hemoglobin completely fills the tubule lumen and outlines the microvilli of the brush border. The penetration of hemoglobin along the intercellular spaces is blocked at the level of the tight junctions (also known as zonula occludens) and does not appear in the adherens junctions (also known as zonula adherens) or in the distended intercellular spaces below the level of the shallow tight junctions. Hemoglobin also has been internalized via large clathrin coated vesicles and appears in endosomes and lysosomes.First demonstration that the tight junction acts as a barrier preventing passage of proteins along the intercellular spaces by forming a seal between adjacent cells. First demonstration of the shallow nature of the tight junctions between epithelial cells in the proximal tubule. Identical labeled image available as CIL# 7623. Image published as Figure 24 in Farquhar and Palade, 1963.
description: In this experiment, hemoglobin was used
as a mass tracer. The rat received two injections, each of 1 gm of 2 X crystallized bovine hemoglobin in ~5 ml saline, administered intraperitoneally, the first at 24 and the last at 16 hours before collecting kidney specimens. Fixative was perfused into the aorta of the rat (2% osmium tetroxide buffered at pH 7.6 with acetate-veronal). Tissue blocks were stained by placing them for 30 minutes in 1 per cent phosphotungstic acid in absolute ethanol prior to infiltration and were embedded in Epon. Thin sections were stained with lead hydroxide. Micrograph was taken at original magnification of 50,000 X with a Siemens Elmiskop I, operating at 60 or 80 kv, with a double condenser, and a 50 µ objective aperture. Digitization process: conversion from a 1200 dpi tiff, 3832 x 3260 pixels. Original image created on June 11, 1962. Original resource provided as a 3.25 x 4 inch lantern slide. Research conducted at The Rockefeller Institute of Medical Research (New York, NY).
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: lead salt; phosphotungstic acid
Processing history: digitized lantern slide
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0hm57gc
title: CIL:7619, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the microtubular nemadesmata that extend deep into the cytosol from the membranelles of the perioral kinetids. Bridges link the plasma membrane to the alveoli. Parasomal sacs occur around the basal bodies and a nascent food vacuole is evident. TEM taken on 3/18/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 13,750X. 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: film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j09w0d22
title: CIL:46297, 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 26669 - 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/j0dz06wz
title: CIL:46311, 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 24588 - 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/j05h7dwf
title: CIL:46313, Homo sapiens. In Cell Image Library

description: Plate 24642 - 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.