cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0hq3xhc
title: CIL:48757, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 3
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j0bg2mk6
title: CIL:48755, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 2
 
Project: 20389
DOI: 10.6075/j0w957sq
title: CIL:48754, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 2
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j0gx4961
title: CIL:48762, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 4
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j0xg9pqr
title: CIL:48763, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 5
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j07m06jg
title: CIL:48761, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 4
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j05h7dv0
title: CIL:48760, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 4
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
description: Item type: confocal microscopy
DOI: 10.6075/j0639pwp
title: CIL:48304, Sprague-Dawley rat. In Cell Image Library

description: Images are acquired from fixed and living heart tissue using fiber-optics and laser-scanning confocal microscopy, respectively. Three sets of images denoted as CCM, FCMtopical, FCMcarrier were stored for subsequent analyses.
description: Preparation: chemically fixed tissue
Imaging mode: confocal microscopy
description: Tissue regions were labeled with a dye carrier affixed to the tip of a fiber-optics microprobe (UltraMiniOWD30; Mauna Kea Technologies). Dye carriers were loaded for 15 min with sodium fluorescein [Fluorescite® (fluorescein injection, USP) 10%; Alcon, Fort Worth, TX, US; 1:1000] prior to imaging. With this imaging protocol, we acquired two-dimensional image sequences of the tissue regions at a lateral resolution, optical sectioning, field of view, frame rate, and z-scan range of 1.4 μm, 7 μm, 186 by 130 μm, 12 Hz and 26 μm, respectively. Example images from these image sequences were stored as FCMcarrier.
DOI: 10.6075/j0fn16ct
title: CIL:48303, Sprague-Dawley rat. In Cell Image Library

description: Preparation: chemically fixed tissue
Imaging mode: confocal microscopy
description: Images are acquired from fixed and living heart tissue using fiber-optics and laser-scanning confocal microscopy, respectively. Three sets of images denoted as CCM, FCMtopical, FCMcarrier were stored for subsequent analyses.
description: CCM images were from fixed rodent tissue preparations acquired using established methods (doi: 10.1161/circimaging.112.000121). In short, rodent hearts were isolated and Langendorff-perfused with 4% paraformaldehyde. Tissue from the atrial working myocardium, sinoatrial node, and atrioventricular node were dissected from the hearts and fluorescently labeled with wheat germ agglutinin conjugated to CF488A (29022-1; Biotium, Hayward, CA; 1:25). Fluorescently labeled tissue preparations were imaged using a conventional laser-scanning confocal microscope (Zeiss LSM5 Duo; Zeiss, Jena, Germany) with a 40x oil immersion lens (NA 1.3). The fluorescent signal was captured using an Argon/2 ion laser (488 nm excitation) and a bandpass filter (505 to 555 nm emission). Three-dimensional image stacks were acquired at a spatial resolution (xyz dimensions), field of view (xy) and a z-scan range of 0.2x0.2x0.2 μm, 204.8x204.8 μm and 50 μm, respectively. Example cross-sections through the image stacks were stored as CCM images.
DOI: 10.6075/j0736r3c
title: CIL:48251, Xenopus laevis, egg. In Cell Image Library

description: Preparation: live reaction of interphase Xenopus egg extract under a cover slip artificial microtubule organizing center
Relation to intact cell: Low-speed lysate; cytoplasmic fraction
Item type: TIRF
Imaging mode: Laser excitation of fluorophore; Detection of fluorescence emission
Data qualification: Processed
description: By taking the negative intensity differences of subsequent frames in the microtubule movie CIL48253, a spatial map of microtubule depolymerization was generated.
description: How the cell cytoplasm is spatially organized is of fundamental interest. In ordinary animal cells the cytoplasm is organized by a radial array of microtubules, called an aster. Aster microtubules are nucleated by the centrosome and elongate to the periphery. We investigated how asters grow in an extremely large cell, the frog egg, using microscopy of an extract system. Asters were initially nucleated at centrosomes, but then additional microtubules nucleated far from the centrosome, apparently stimulated by preexisting microtubules. The resulting growth process allows asters to scale to the size of huge egg cells while maintaining a high density of microtubules at the periphery. Microtubule-stimulated microtubule nucleation might be a general principle for organizing large cells.
 
 Note: Negative intensity difference of Movie S4
DOI: 10.6075/j0bv7gsx
title: CIL:48201, Mus musculus, parietal cell, zymogen, mucus. In Cell Image Library

description: Preparation: Paraformaldehyde
Item type: micrograph
Imaging mode: modes of light microscopy
description: Light micrograph, alcian blue PAS staining of gastric mucosa from N 18 month old gastrick H,K,ATPase null mouse, 100 x
DOI: 10.6075/j02v2dpc
title: CIL:45962, 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 25945 - 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/j0jd4vcb
title: CIL:45959, 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 25939 - 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/j0dn457f
title: CIL:48602, Mus musculus. In Cell Image Library

description: Item type: micrograph
Imaging mode: modes of light microscopy
description: Preparation: Paraformaldehyde
Stain1: PAS
Stain2: Alcian blue
Embed: Paraffin
Section: 5 microns
Species: musculus (mixed 129SvJ and Black Swiss)
Gender: male
Age: 12 months
Subspecies or gene: gastric, H,K, aATPase alpha -/-
Organ: stomach
Tissue: gastric mucosa, greater curvature, hyperplasia, mucus cells, cysts
description: Light micrograph, alcian blue PAS staining of gastric mucosa from 12 month mouse, 100 x
DOI: 10.6075/j0jd4x07
title: CIL:48601, Mus musculus, ciliated cell in gastric epithelium of KO mouse. In Cell Image Library

description: Transmission electron micrograph of gastric HKAtpase alpha KO mouse ciliated possible brush cell in the greater curvature of the stomach band on cilia reminiscent of cilia in respiratory epithelium animation with three ciliary zones identified
description: Preparation: Glutaraldehyde and paraformaldehyde in phosphate buffer
Stain1: 1% osmium tetroxide
Stain2: lead citrate and uranyl acetate
Embed: Spurr's resin
Voltage: 60kv
Magnification: 2500x4
Section: 50-100 nm thick
Species: musculus (mixed 129SvJ and Black Swiss)
Gender: female
Age: 10.5 weeks
Subspecies or gene: gastric, H,K, aATPase alpha -/-
Organ: stomach
Tissue: gastric mucosa, greater curvature
description: Imaging mode: transmission electron microscopy (TEM)
DOI: 10.6075/j0s75dzd
title: CIL:48501. In Cell Image Library

description: Item type: quantitative differential interference contrast microscopy
Data qualification: Processed
description: Equipment used: We used newly developed orientation-independent differential interference contrast (OI-DIC) technique (US Patent 7564618). The image was taken by Olympus BX-61 microscope equipped with 40x/0.75NA objective lens.
description: Biological Context and Probe: Herpetosiphon aurantiacus is a filamentous non-phototrophic bacterium that exhibits gliding motility and is capable of predation on other bacteria. The picture brightness is linearly proportional to the dry mass distribution.
DOI: 10.6075/j02b8z5c
title: CIL:48351, Sprague-Dawley rat. In Cell Image Library

description: CCM images were from fixed rodent tissue preparations acquired using established methods (doi: 10.1161/circimaging.112.000121). In short, rodent hearts were isolated and Langendorff-perfused with 4% paraformaldehyde. Tissue from the atrial working myocardium, sinoatrial node, and atrioventricular node were dissected from the hearts and fluorescently labeled with wheat germ agglutinin conjugated to CF488A (29022-1; Biotium, Hayward, CA; 1:25). Fluorescently labeled tissue preparations were imaged using a conventional laser-scanning confocal microscope (Zeiss LSM5 Duo; Zeiss, Jena, Germany) with a 40x oil immersion lens (NA 1.3). The fluorescent signal was captured using an Argon/2 ion laser (488 nm excitation) and a bandpass filter (505 to 555 nm emission). Three-dimensional image stacks were acquired at a spatial resolution (xyz dimensions), field of view (xy) and a z-scan range of 0.2x0.2x0.2 μm, 204.8x204.8 μm and 50 μm, respectively. Example cross-sections through the image stacks were stored as CCM images.
description: Images are acquired from fixed and living heart tissue using fiber-optics and laser-scanning confocal microscopy, respectively. Three sets of images denoted as CCM, FCMtopical, FCMcarrier were stored for subsequent analyses.
description: Preparation: chemically fixed tissue
Imaging mode: confocal microscopy
DOI: 10.6075/j0xk8fp2
title: CIL:48305, Sprague-Dawley rat. In Cell Image Library

description: Images are acquired from fixed and living heart tissue using fiber-optics and laser-scanning confocal microscopy, respectively. Three sets of images denoted as CCM, FCMtopical, FCMcarrier were stored for subsequent analyses.
description: Preparation: chemically fixed tissue
Imaging mode: confocal microscopy
description: The imaging protocol was based on topical application of 3 or 10 kDa dextran conjugated to Alexa Fluor 488 (Invitrogen, Carlsbad, CA, 125 μg/mL) via pipette to the tissue regions prior to imaging. Immediately following, images were acquired using the fiber-optics confocal microscopy system equipped with a custom fiber-optics microprobe (UltraMiniO; Mauna Kea Technologies, Paris, France). Using this imaging protocol, we acquired two-dimensional images sequences of the tissue regions at a lateral resolution (xy dimensions), optical sectioning (z), field of view (xy), frame rate, and z-scan range of 1.8 μm, 10 μm, 169 by 120 μm, 12 Hz and 50 μm, respectively. Example images from image sequences were stored as FCMtopical.
DOI: 10.6075/j09p30h0
title: CIL:41657, Portulaca, seed. In Cell Image Library

description: Stereomicrograph of a Purslane (Portulaca) seed. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: stereo microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in intrinsic optical density