cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j00g3jj6
title: CIL:45821, Homo sapiens. In Cell Image Library

description: Plate 24789 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.6075/j0c8286c
title: CIL:39031, Volvox, gamete. In Cell Image Library

description: Light micrograph of Volvox taken using Rheinberg illumination. Volvox form large (approximately 500 µm) spherical colonies that can contain up to 15,000 biflagellate, photosynthetic cells embedded in their gelatinous walls. The colonies are hollow (coenobia) and often found with daughter colonies, and/or groups of gametes lying inside them. Beating of the flagella is strongly co-coordinated so that, for instance, colonies can rapidly react to a light source by swimming toward it. They are mainly found in freshwater ponds. The image is of a live specimen captured with a 0.5 microsecond flash.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: Rheinberg illumination
Parameter imaged: elastic scattering of photons; absorption of illumination
Source of contrast: differences in amount of elastic light scattering; differences in intrinsic optical density
Visualization methods: Rheinberg filters
Processing history: unprocessed raw data
description: B0007761 Colony of volvox with eight daughter coenobia. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/

See the following website for a description of Rheinberg illumination http://micro.magnet.fsu.edu/primer/techniques/rheinberg.html
DOI: 10.6075/j02v2dxh
title: CIL:26573, Homo sapiens, epithelial cell, renal pigment epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: widefield illumination; time lapse microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Movie raw file of RPE-1 cells expressing GFP-alpha-tubulin and depleted for pVHL (Von Hippel-Lindau) by ectopic expression of shRNAmir against VHL. Video used to manually track MTs and determine growth speed and shrinkage time. Cells on round coverslips were transferred to a homemade holding device, and 600 µl of the appropriate medium was added. The video was acquired with a microscope (IX70 Delta Vision Spectris; Olympus), temperature-controlled at 37C, using a 100× NA 1.4 differential interference contrast (DIC) oil Plan-Apochromat objective, ex 470 em 520, and a camera (CoolSNAP HQ; Roper Industries) with an exposure time of 200 ms and a frame rate of 2Hz. Acquisition software used was SoftWoRx version 3.3.4 (Applied Precision). This video corresponds to J Cell Biol. 2010. 190: 991-1003--Supplementary Figure 1.
DOI: 10.6075/j02n50z2
title: CIL:36729, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
description: A print of the negative was scanned and processed in Photoshop. This image is suitable for qualitative analysis. A high resolution version of this image in the library (CIL:40560) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Higher magnification of acidosomes docked at the nascent digestive vacuole membrane. The E-fracture face is relatively IMP free while the P-fracture face has many large IMPs as well as some sizable pits where chunks of this leaflet seem to have stuck to the E-face. Tiny pits on the E-face indicate the removal of individual IMPs from this leaflet. An indentation of the membrane into the lumen of the acidosome shows IMPs on its exposed P-face; which, if any, of these IMPs are V-ATPases is not known. TEM taken on 5/26/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.2µm. Published in J. Cell Sci. 106:411-422, 1993. Adapted with permission.
DOI: 10.6075/j0sb455v
title: CIL:45847, Homo sapiens. In Cell Image Library

description: Plate 25432 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.6075/j0z60ndf
title: CIL:40901, Didinium nasutum, Paramecium sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: chemically fixed tissue; lyophilized specimen; Parducz fixative; Au/Pd metal sputter-coat
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: illumination by electrons; secondary_electron imaging
Parameter imaged: illumination by electrons; secondary electron generation; secondary_electron imaging
Source of contrast: detection of electrons
Visualization methods: shadowing and plating
Processing history: recorded image; film
Data qualification: Raw
description: Didinium captures Paramecium. The cytostome opens at the end of the proboscis to accept its prey. Also showing metachronous waves of cilia within the two characteristic ciliary girdles of Didinium nasutum; the waves on Paramecium may be paralyzed due to the effects of the attached toxicysts. This micrograph was taken in 1968 by G. Antipa on a Cambridge Mark IIA operating at 20kV. The negative magnification is 485X. Further details are available at Wessenberg, H. and Antipa, G. 1970. Capture and ingestion of Paramecium by Didinium nasutum. J. Protozool. 17:250-270.
DOI: 10.6075/j07h1h8z
title: CIL:13680, Chlorocebus aethiops. In Cell Image Library

description: To study the cellular consequences of misfolding of plasma membrane proteins, a transmembrane model protein that was constitutively targeted to the plasma membrane was developed for use as a reporter molecule. The reporter consisted of a C-terminally truncated CD4, incorporating a flexible cytoplasmic linker (CD4tl), fused to the N-terminal DNA-binding domain of the wild type (wt) bacteriophage lambda repressor (CD4tl-lambda) or L57C mutant repressor (CD4tl-lambdaC). The CD4tl-lambdaC cytosolic domain was largely in native state at 26°C but predominantly nonnative state at 37°C thus allowing the use of thermal shifts to follow the fate of unfolded proteins. In this image, one of six of a group from Figure 1 of Pirjo et al., JCB 2010, the expression of the mutant plasma membrane reporter, CD4tl-lambdaC, at 26 degrees is seen with CD4 antibody (green) in a detergent-permeabilized COS7 cell. At this temperature, the folding and processing of this mutant membrane reporter allows targeting to the plasma membrane. The cell is co-labeled with an ER marker, calreticulin antibody (red).
description: Preparation: crosslinking-fixative fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 555
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j02j69sw
title: CIL:36152, damselfly, flight muscle cell. In Cell Image Library

description: Longitudinal and cross sections showing ribbon like myofibrils regularly alternating with layers of mitochondria and SR/T tubules. Dyads are located in a grove of the mitochondrial surface. Negatives aere scanned on nikon 8000 at 4000dpi/6.3 micron scan step size, then reduced in size 4X for upload, for an effective pixel size of 25 micron.
 
 Technical details:
 Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer (pH7.2). Stored at 4C for several days. Muscle dissected out. Rinsed 3Xin buffer, postfixed in 2% PsO4 in buffer, for 1.5 hrs; rinsed 3 times in water, en-block stained in saturated aqueous uranyl acetate, embedded in Spurr. Thin sections stained in uranyl acetate and lead and examined in a Philips 410 Microscope.
 
 Reference for the image:
Loesser, K.E., Castellani, L. and Franzini-Armstrong, C. Disposition of junctional feet in muscles of invertebrates. J. Muscle Research Cell Motility 13:161-173, 199
description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j02z14wd
title: CIL:38892, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis.
description: A grazing section through the cell‚Äôs surface shows segments of six rows of cilia running across the figure sectioned superfically at the top and deeper into the cell as one progresses down the figure. Crests of the polygonal ridges appear at the top of the figure where the expanded alveoli fill most of the space in the surface depressions. Septa, the borders of adjoining alveolar sacs, run between basal body/cilium complexes along a kinety. Trichocyst tips penetrate into the lateral ridges that separate the concave depressions of a kinety. Within the cortical cytosol a more superficial system of striated bands connects the slopes of adjacent ridges, laterally, longitudinally and diagonally. Internal to the striated bands is a meshwork of centrin-containing fibrous bundles called the infraciliary lattice. This meshwork surrounds the proximal half of basal bodies but does not insert into the pellicular membranes. Collidine-buffered fixative. TEM taken on 7/8/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X.
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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0ww7ghn
title: CIL:46706, Homo sapiens, parenchymal cell. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
description: Normal morphology of two peroxisomes (marked P) in a human liver parenchymal cell. They are contiguous with a narrow endoplasmic reticulum cisterna; this relationship is frequent. The image also shows a large dark lysosome with a membrane, contrasted with cerium by acid phosphatase activity. Several mitochondria are seen, and in the cytosol many glycogen rosettes typical for liver of a fed person; and a few fat droplets (no membrane). Marker = 0.5 µm.
description: Prefixation in cold glutaraldehyde, acid phosphatase reaction with cerium, post fixation in OsO4.
DOI: 10.6075/j0j38rfd
title: CIL:36656, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; microtome-sectioned tissue; 00000018
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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: In the contact area between two conjugating cells the tips of the ridges all fuse forming openings between the two cells. TEM taken on 3/4/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 8,500X. Bar = 0.5µm.
DOI: 10.6075/j0sx6bsm
title: CIL:47372, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 5 - Venular data)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
DOI: 10.6075/j0pn954g
title: CIL: 52143, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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.
DOI: 10.6075/j0cc108m
title: CIL: 52918, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 11, z=11 from SC_007
description: One z layer of a z-stack at the given image
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j0n29vwf
title: CIL:25516, Drosophila melanogaster, salivary gland. In Cell Image Library

description: Salivary glands from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film, are transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV.
description: Whole mount squash of interphase nucleus from Drosophila salivary gland. Image was taken with a High Voltage EM at a tilt angle of 55 degrees. The accompanying grouped image, taken at 43 degrees forms a stereo pair, providing an oblique 3D view of the nucleus.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data