cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0j9654n
title: CIL:13719, Homo sapiens, endothelial cell. In Cell Image Library

description: PINK1-YFP R98F (green) is localized to mitochondria in the absence of the mitochondrial depolarizing agent CCCP (carbonyl cyanide-m-chlorophenyl hydrazone). The R98F mutation in PINK1-YFP partially inhibits proteolytic cleavage. When fixed cells are permeabilized with 0.005% digitonin, the antibody to GFP (red) (used to identify PINK1-YFP R98F) is unable to reach and bind PINK1-YFP R98F, but the antibody to Tom20 (white), a mitochondrial outer membrane marker, is able to bind its epitope. This demonstrates that PINK1 R98F is located inside mitochondria. PINK1-YFP R98F transfected HeLa cells were treated with DMSO for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.005% digitonin. Primary antibodies used were: anti-GFP polyclonal Ab (Invitrogen) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4c, 4th row from top, and is part of a differential permeabilization assay to determine submitochondrial localization of PINK1 R98F and that is further described in Fig 4c of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j08s4pck
title: CIL: 51873, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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.
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
DOI: 10.6075/j0ms3rgg
title: CIL:13718, Homo sapiens, endothelial cell. In Cell Image Library

description: PINK1-YFP R98F (green) is localized to mitochondria in the absence of the mitochondrial depolarizing agent CCCP (carbonyl cyanide-m-chlorophenyl hydrazone). The R98F mutation in PINK1-YFP partially inhibits proteolytic cleavage. When fixed cells are unpermeabilized (not treated with detergent), antibodies to GFP (red) (used to identify PINK1-YFP R98F), and Tom20 (white), a mitochondrial outer membrane marker, are unable to reach and bind their epitopes. PINK1-YFP R98F transfected HeLa cells were treated with DMSO for 3 hrs, fixed with 4% paraformaldehyde and not permeabilized. Primary antibodies used were: anti-GFP polyclonal Ab (Invitrogen) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4c, 4th row from top, and is part of a differential permeabilization assay to determine submitochondrial localization of PINK1 R98F and that is further described in Fig 4c of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0gh9gp4
title: CIL:13691, Homo sapiens. In Cell Image Library

description: This is one of six images in Figure 6 in Apaja et al., JCB 2010 that shows the fate of various model membrane proteins, that are either folded or in the unfolded state at the plasma membrane, expressed in stable tetracycline-inducible Flp-In T-Rex HEK293 cell lines. The three model membrane proteins were chimeras of the CD4 surface receptor consisting of 1.) a C-terminally truncated CD4 that contained a flexible cytoplasmic linker (CD4tl), 2.) a CD4tl fused to the N-terminal DNA-binding domain of the wild type bacteriophage lambda repressor (CD4tl-lambda), and 3.) a CD4tl fused to a L57C mutant lambda 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. To examine the post-endocytic distribution of CD4 chimeras, membrane proteins were labeled by CD4 Ab capture for 20 mins in live cells at 37°C and chased for 1 h in the absence of extracellular Ab before fixation and labeling with secondary antibody to localize the internalized CD4 chimeras (green). Endosomes were labeled with 10 µg/ml Alexa Fluor 594-labeled transferrin uptake for 1 h at 37°C (red). Fluorescence micrographs were obtained by a confocal microscope (LSM510 or LSM710; Carl Zeiss, Inc.) equipped with a Plan-Apochromat 63×/NA 1.4 objective in multitrack mode. This single optical section shows that internalized CD4tl-lambdaC protein, the model membrane mutant that does not fold properly, does not co-localize with endosomes. This is in contrast to internalized CD4tl and CD4tl-lambda, seen in companion images in this group, and normal membrane receptors.
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; distribution of epitope
Visualization methods: Alexa Fluor 488; Alexa Fluor 594
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j08914j7
title: CIL:34912. In Cell Image Library

description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data
DOI: 10.6075/j0m907cz
title: CIL:13689, Homo sapiens. In Cell Image Library

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; distribution of epitope
Visualization methods: Alexa Fluor 488; Alexa Fluor 594
Processing history: unprocessed raw data
Data qualification: Raw
description: This is one of six images in Figure 6 in Apaja et al., JCB 2010 that shows the fate of various model membrane proteins, that are either folded or in the unfolded state at the plasma membrane, expressed in stable tetracycline-inducible Flp-In T-Rex HEK293 cell lines. The three model membrane proteins were chimeras of the CD4 surface receptor consisting of 1.) a C-terminally truncated CD4 that contained a flexible cytoplasmic linker (CD4tl), 2.) a CD4tl fused to the N-terminal DNA-binding domain of the wild type bacteriophage lambda repressor (CD4tl-lambda), and 3.) a CD4tl fused to a L57C mutant lambda 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. To examine the post-endocytic distribution of CD4 chimeras, membrane proteins were labeled by CD4 Ab capture for 20 mins in live cells at 37°C and chased for 1 h in the absence of extracellular Ab before fixation and labeling with secondary antibody to localize the internalized CD4 chimeras (green). Endosomes were labeled with 10 µg/ml Alexa Fluor 594-labeled transferrin uptake for 1 h at 37°C (red). Fluorescence micrographs were obtained by a confocal microscope (LSM510 or LSM710; Carl Zeiss, Inc.) equipped with a Plan-Apochromat 63×/NA 1.4 objective in multitrack mode. This single optical section shows that internalized CD4tl protein co-localizes with endosomes, like other plasma membrane receptors. This contrasts with the behavior of the internalized, unfolded mutant CD4tl-lambdaC, seen in a companion image in this group.
DOI: 10.6075/j0zg6r0b
title: CIL:13685, 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 control reporter, CD4tl-lambda, at 37 degrees is seen with CD4 antibody (green) in a non-permeabilized COS7 cell and the apparent plasma membrane targeting shows the value of this model plasma membrane protein. The ER marker, calreticulin antibody (red), is not apparent here because lack of detergent-permeabilization limited access of the antibody to the ER.
description: Preparation: crosslinking-fixative fixed tissue
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/j07d2sqf
title: CIL:45970, 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 25983 - 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/j0gt5kwn
title: CIL:13684, Chlorocebus aethiops. In Cell Image Library

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
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 control reporter, CD4tl-lambda, at 37 degrees is seen with CD4 antibody (green) in a detergent-permeabilized COS7 cell and the apparent plasma membrane targeting shows the value of this model plasma membrane protein. The cell is co-labeled for an ER marker, calreticulin antibody (red)..
DOI: 10.6075/j0862fc2
title: CIL:27228, Fundulus heteroclitus, epidermal cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; dehydrated in ethanol
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: uranyl salt; lead salt
Processing history: unprocessed raw data
description: Rough endoplasmic reticulum and Golgi in the epidermal cell of Fundulus heteroclitus scale. Endoplasmic reticulum studded with protein-manufacturing ribosomes form a continuous network along the periphery of this section of the cell. Along the surface of some of the ER folds are energy-generating mitochondria. Deeper into the cell are stacks of cisternae forming the Golgi. Vesicles packaged by the Golgi are visible at the peripheries of these stacks and are found scattered throughout the cytoplasm.
description: Fundulus heteroclitus scales were chemically fixed with 2.5% glutaraldehyde, 2% formaldehyde in 0.1M cacodylate buffer (pH 7.3), then post-fixed in 4% osmium tetroxide and stained en bloc in 1% uranyl acetate. The scales were then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph was imaged using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80 kV.
DOI: 10.6075/j0p26ww1
title: CIL:13681, 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 37 degrees is seen with CD4 antibody (green) in a detergent-permeabilized COS7 cell. The intracellular processing of this nonnative, thermally unfolded protein nearly completely limits its targeting to the plasma membrane. This 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/j06h4g4k
title: CIL:13679, Drosophila melanogaster, motor neuron. In Cell Image Library

description: The JNK phosphatase puckered, whose expression can be reported via a lacZ enhancer trap, is expressed in very low levels in uninjured neurons; however, nerve crush induces a dramatic increase in puc-lacZ expression in injured motoneurons. This image stack shows puc-lacZ (green) and neuronal nuclei (red) in an uninjured third instar larva. Wandering third instar larvae were dissected in PBS and fixed in either 4% paraformaldehyde in PBS or Bouin's fixative for 15–30 min. Primary antibodies used were: rat anti-elaV (7E8A10, Developmental Studies Hybridoma Bank) and mouse anti-lacZ (40-1a, DSHB). Secondary antibodies were Alexa 488 anti-mouse and Cy3 anti-rat. Confocal images were collected at room temperature on a spinning-disk confocal system (PerkinElmer) consisting of a scanner (Nipkow CSU10; Yokogawa) and an electron microscopy charge-coupled device camera (C9100-50; Hamamatsu Photonics) mounted on an inverted microscope (Axio Observer; Carl Zeiss, Inc.) with 25× 0.8 NA multi and 40× 1.3 NA, 63× 1.5 NA, and 100× 1.46 NA oil objectives. Similar settings were used to collect all compared genotypes. All imaging and quantification were conducted with Volocity software (PerkinElmer). This image stack corresponds to Fig 1D in J Cell Biol. 2010. 191: 211-223. Images in Fig 1 include CIL#s 13676, 13677, 13678, 13679.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; beta-galactosidase; Alexa Fluor 488; Cy3
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0765f56
title: CIL: 54642. In Cell Image Library

description: This image displays degenerating neuron with PHF and lipofucscin.
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.
description: Item type: Serial section
Imaging mode: transmission electron microscopy (TEM)