cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0z036rm
title: CIL:46021, 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 26531 - 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/j0w66jbz
title: CIL:45978, 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 25991 - 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/j0h70fnd
title: CIL: 54724. In Cell Image Library

description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope. Stereo viewing and computer assisted serial reconstruction techniques were employed to visualize three-dimensional relationships among cytoplasmic components of cortical neurons.
description: Item type: EM tomogram
Imaging mode: transmission electron microscopy (TEM)
description: 2D survey of cerebral cortex.
DOI: 10.6075/j0vx0fzf
title: CIL: 51821, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
DOI: 10.6075/j0jh3kg1
title: CIL:1046, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j06t0k9n
title: CIL:37182, Rattus, kidney cell, fenestrated cell, glomerular endothelial cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: 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
description: Relevant citations: 
Kanwar, Y.S. and M.G. Farquhar. 1979. J. Cell Biol. 81:137-153.
Farquhar, M.G., S.L. Wisssig and G.E. Palade. 1961 . J. Exp. Med. 113:47-66.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification X14,000.
description: Transmission electron micrograph of a rat kidney filtration barrier. This tangential section illustrates the fenestrated endothelium and basement membrane. The series of images in this group have particular historic and cell biologic importance for determining the role of the glomerular basement membrane in urinary filtration, especially the charge properties and size selectivity in retention of proteins in the circulation. The images here clearly show the glomerular filtration barrier. The study also elucidated the role of the basement membrane in some forms of nephrosis. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j03r0rhs
title: CIL:37201, Rattus, cardiac muscle cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: 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
Processing history: unprocessed raw data
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x17,000.
description: Transmission electron micrograph of longitudinal section of rat heart ventricle. A portion of a nucleus is seen at upper right, with a region of closely packed mitochondria extending to lower left, flanked by myofibrils. Small, darkly staining glycogen granules are also prominent.
 Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0g16063
title: CIL:41730, Cricetulus griseus, ovary. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: CHO cells at metaphase were treated with 50% D2O, fixed with glutaraldehyde, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranyl acetate and lead citrate for HVEM observation at 1MeV. See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High Voltage EM image of CHO metaphase chromosomes from a 'thick' section of metaphase-arrested cells treated with D20 to stabilize microtubules. This image was recorded with a specimen tilt of 55 degrees. The accompanying grouped image had a tilt of 45 degrees to create a stereo pair providing an oblique 3D view of the chromosomes.
DOI: 10.6075/j0zw1jkq
title: CIL:37181, Rattus, kidney cell, glomerular endothelial cell, podocyte. In Cell Image Library

description: Relevant citations: 
Kanwar, Y.S. and M.G. Farquhar. 1979. J. Cell Biol. 81:137-153.
Farquhar, M.G., S.L. Wisssig and G.E. Palade. 1961 . J. Exp. Med. 113:47-66.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi.
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: 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
description: Transmission electron micrograph of rat kidney filtration barrier. Image is low magnification vies of the basement membrane filtration slits, urinary space, and the glomerular filtration capillary lumen. The series of images in this group have particular historic and cell biologic importance for determining the role of the glomerular basement membrane in urinary filtration, especially the charge properties and size selectivity in retention of proteins in the circulation. The images here clearly show the glomerular filtration barrier. The study also elucidated the role of the basement membrane in some forms of nephrosis. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0f47ms8
title: CIL:37185, Rattus, hepatocyte. In Cell Image Library

description: Transmission electron micrograph of the junctional complexes at the intersection of three hepatocytes. This image was taken from liver tissues from an ethanol fed rat and also shows the bile canaliculus. Smooth endoplasmic reticulum and associated vesicles are prominent. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x10,050.
description: Preparation: chemically fixed tissue
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
Processing history: unprocessed raw data
DOI: 10.6075/j0wm1c13
title: CIL:37163, Mus musculus, epithelial cell. In Cell Image Library

description: Transmission electron micrograph of a microvilli at the apex of a mouse intestine. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi.
description: Preparation: chemically fixed tissue
Relation to intact cell: 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
Processing history: unprocessed raw data
DOI: 10.6075/j0zc827x
title: CIL:41708, Cricetulus griseus, ovary. In Cell Image Library

description: High Voltage (1MeV) EM image of a metaphase chromosome isolated from CHO cells using a non-aqueous technique, squashed in 1:1 acetic acid:ethanol and transferred to an EM grid. A chromatid pair occupies the center of the image. This micrograph was captured at a specimen tilt of 55 degrees. The accompanying image has a tilt of 45 degrees, creating a stereo pair that provides an oblique stereo view of the chromatids.
description: Preparation: chemically fixed tissue
Relation to intact cell: squash
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells were metaphase arrested with thymidine followed by colcemid, then exposed to a low ionic strength swelling medium (0.07M phosphate bufferin 50% D2O). Chromosomes were isolated by the non-aqueous hexylene glycol technique of Wray and Stubblefield, squashed in 1:1 acetic acid:ethanol,stained, and transferred to an EM grid.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
DOI: 10.6075/j0zc81jj
title: CIL:37204, Cavia porcellus, cardiac muscle cell. In Cell Image Library

description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x40,000.
description: Preparation: chemically fixed tissue
Relation to intact cell: 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
Processing history: unprocessed raw data
description: Transmission electron micrograph of section of cardiac muscle from guinea pig right atrium. A portion of nucleus is seen at upper right, with a centriole close to the nuclear envelope. Also seen in the cytoplasm is a portion of a mitochondrion at lower left several homogeneously atrial granules and numerous darkly staining glycogen granules. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0d50km0
title: CIL:37260, Chlamydomonas reinhardtii. In Cell Image Library

description: Preparation: chemically fixed tissue; tissue in plastic embedment
Relation to intact cell: 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
Processing history: unprocessed raw data
description: An electron micrograph of a cross section of a flagellum from the unicellular alga Chlamydomonas (Yellow strain) showing the characteristic 9-fold symmetry. This section, close to the basal body does not show the 2 central microtubules that occur in the axoneme proper. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification x93,000.
DOI: 10.6075/j0rv0mbt
title: CIL:37120, Cavia porcellus, pancreas cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); electron microscope autoradiograph
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; metabolically incorporated radioisotope
Processing history: unprocessed raw data
description: Electron microscope autoradiograph taken 20 min after injection showing that the radiographic label has migrated from the rough endoplasmic reticulum to the Golgi complex. Most of the radioactive grains are over condensing vacuoles and the perpheral clusters of small vesicles have much less activity. Image corresponds to Figure 5 in J. Cell Biol. 20:473-495. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Anesthetized animals were intravenously injected with 1-5 millicuris of DL-leucine 4,5-H^3 with a specific activity of 3570 mc/mM. At times ranging from 4 min to 15 hrs after injection the pancreas was removed and fixed in osmium tetroxide. Tissue was embedded in methacrylate, sectioned, and post-stained with uranyl acetate. 

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x30,000.
DOI: 10.3886/e239484
title: HIFLD OPEN Lateral Buoys (USACE IENC)

description: The USACE IENCs coverage area consists of 7,260 miles across 21 rivers primarily located in the Central United States. IENCs apply to inland waterways that are maintained for navigation by USACE for shallow-draft vessels (e.g., maintained at a depth of 9-14 feet, dependent upon the waterway project authorization). Generally, IENCs are produced for those commercially navigable waterways which the National Oceanic and Atmospheric Administration (NOAA) does not produce Electronic Navigational Charts (ENCs). However, Special Purpose IENCs may be produced in agreement with NOAA.
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025. (Downloaded 08/26)
DOI: 10.6075/j0k35sbn
title: CIL:37232, Cavia porcellus, pancreatic cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: 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
Processing history: unprocessed raw data
description: Early transmission electron micrograph showing intracisternal granules with an electron density equal to that of zymogen granules found in rough endoplasmic the reticulum lumen (cisternae) of animals fed after starvation or after intense in vitro stimulation with secretagogues. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Additional reference: Palade, G.E. 1956. Intracisternal granules in the exocrine cells of the pancreas. J. Biochem. Biophys. Cytol. 2:417-422. Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x13,000
DOI: 10.3886/e239484v1
title: HIFLD OPEN Lateral Buoys (USACE IENC)

description: The USACE IENCs coverage area consists of 7,260 miles across 21 rivers primarily located in the Central United States. IENCs apply to inland waterways that are maintained for navigation by USACE for shallow-draft vessels (e.g., maintained at a depth of 9-14 feet, dependent upon the waterway project authorization). Generally, IENCs are produced for those commercially navigable waterways which the National Oceanic and Atmospheric Administration (NOAA) does not produce Electronic Navigational Charts (ENCs). However, Special Purpose IENCs may be produced in agreement with NOAA.
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025. (Downloaded 08/26)