cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0r78ct1
title: CIL:48767, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

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 - 6
 
Project: 20389
description: Item type: confocal microscopy
DOI: 10.6075/j0ms3rbp
title: CIL:48764, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

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 - 5
 
Project: 20389
description: Item type: confocal microscopy
DOI: 10.6075/j0tt4pkk
title: CIL:45964, Homo sapiens. In Cell Image Library

description: Plate 25955 - 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/j01g0k4d
title: CIL:41569, Elphidium crispum. In Cell Image Library

description: Brightfield image of protozoan Elphidium crispum found growing on the Dorset coast of England. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in intrinsic optical density
Visualization methods: visualization of contiguous regions
DOI: 10.6075/j0f18xm3
title: CIL:41566, Claviceps, Triticum aestivum, fungal cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
description: This confocal micrograph shows wheat stigma (green) infected with Claviceps fungus (yellow). The image was captured with a confocal microscope using a 40X objective. A related image is available as CIL 38806. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j0bc3x7s
title: CIL:12158, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at metaphase. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is a central z-slice. Localization of exogenous TrAP-INCENP (red) plus endogenous CENP-A(green) in INCENP-OFF cells expressing TrAP-INCENP-W766G. Chromosomes stained with DAPI (blue). See Fig 4F panel 1 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0bp01hk
title: CIL:12164, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Anaphase localization of exogenous TrAP-INCENP (red) plus endogenous Aurora B (green) and DNA (blue) in INCENP-OFF cells expressing mutant TrAP-INCENP W766G. See Fig 6B panel 5 in Xu et al. 2009 J Cell Biol 187, 637-653.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
DOI: 10.6075/j0348j46
title: CIL:12162, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Metaphase cell localization of exogenous TrAP-INCENP (red) plus endogenous CENP-A (green) and DNA (blue) in INCENPOFF cells expressing TrAP-INCENP WT. See Fig 6A panel 9 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0js9p6q
title: CIL:12157, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at metaphase. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is a central z-slice. Localization of exogenous TrAP-INCENP (red) plus endogenous Aurora B(green) in INCENP-OFF cells expressing TrAP-INCENP-W766G. Chromosomes stained with DAPI (blue). With this INCENP mutation, Aurora B is excluded from the chromosomes. See Fig 4E panel 1 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0nz86h7
title: CIL:41561, Mus musculus, astrocyte. In Cell Image Library

description: Adult mouse hippocampus, a region of the brain involved in learning and memory, showing reactive astroglia (pale yellow) that have proliferated and enlarged in response to neuronal activity over time. The image was created from a confocal microscopy Z-stack of 7 slices. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Processing history: z stack projection
DOI: 10.6075/j01n7zvr
title: CIL:12154, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at metaphase. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice.Localization of phosphorylated histone H3-S10ph (red) and H3S28ph in a metaphase cell with the inner centromere protein INCENP on. Chromosomes stained with DAPI are shown in blue. See Fig 2A panel 9 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0vd6x9t
title: CIL:41556, Eupholus, epithelial cell. In Cell Image Library

description: Darkfield image of dried thorax scales from a Eupholus weevil. The image was taken at 10X and is composed of a stack of 80 images. Honorable Mention, 2011 Olympus BioScapes Digital Imaging 
 Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: dark-field microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
DOI: 10.6075/j02806dp
title: CIL:41488, Acacia dealbata, pollen. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; ethanol dehydration
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions; shadowing and plating
Processing history: colorized
description: The image was collected on a ZEISS DSM 960A using a SE detector and colorized using Adobe Photoshop.
description: Colorized scanning electron micrograph of pollen (blue) in anther (green) held by the filament (pink ) from Acacia dealbata grown in Ecuador, Provincia Pichincha
DOI: 10.6075/j0gx498x
title: CIL:12265, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Metaphase localization of CENP-T(green) at centromeres during mitosis in INCENP OFF cells. Alpha-tubulin is red and DAPI (DNA) is blue See Fig 7D panels 13-16 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0dj5db1
title: CIL:14006, Homo sapiens. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: single-spot confocal microscopy
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: Hoechst 33342; Alexa Fluor 488; Alexa Fluor 568
description: Hela cells were treated with anti-SENP6 siRNA and synchronized by DTB for 48 hours. Cells were fixed and stained for kinetochore proteins Hec1 (green, Alexa Fluor 488 conjugated secondary Ab). Cells were simultaneously stained for centromeres (CREST, red, Alexa Fluor 568 conjugated secondary Ab) and Hoechst 33342 (blue).

Fluorescence microscopy was performed at RT on a confocal microscope (LSM510 Meta; Carl Zeiss, Inc.) equipped with a 100× Plan-Apochromat objective. A543 nm HeNe laser (5 mW output; detection LP560 nm) was used for detection of Alexa Fluor 568–labeled antibodies. The 488nm line of an Argon laser (25 mW nominal output; detection BP 505–530 nm) was used for analysis of Alexa Fluor 488–labeled antibodies. Hoechst 33258 images were captured using the 364nm line of an ion laser (Enterprise II ML UV; Coherent, Inc.; 80 mW nominal output; detection BP 385–470 nm).

Image Reference: PMID 20212317
DOI: 10.6075/j0rf5sr1
title: CIL:12166, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Aurora B localizes to centromeres in early mitosis, but fails to transfer to the spindle at anaphase in wild type clone 18 cells grown in the Aurora B inhibitor ZM447439. Cells were stained for Aurora B (green), plus alpha-tubulin (red) and DAPI for DNA (blue). See Fig 6E panel 1 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0zg6qzg
title: CIL:12165, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Metaphase cell localization of exogenous TrAP-INCENP (red) plus endogenous Aurora B (green) and DNA (blue) in INCENPOFF cells expressing TrAP-INCENP WT. See Fig 6A panel 1 in Xu et al. 2009 J Cell Biol 187, 637-653.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
DOI: 10.6075/j0kd1wnh
title: CIL:12160, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Cell of the DT40 chicken B lymphocyte line at metaphase. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is a central z-slice. Localization of exogenous TrAP-INCENP (red) plus endogenous CENP-A (green) in INCENP-OFF cells expressing TrAP-INCENP-F802A. Chromosomes stained with DAPI (blue). See Fig 4H panel 1 in Xu et al. 2009 J Cell Biol 187, 637-653.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
DOI: 10.6075/j0p849mq
title: CIL:12170, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line in mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. INCENP localizes to centromeres in early mitosis, but fails to transfer to the spindle at anaphase in wild type clone 18 cells grown in the Aurora B inhibitor ZM447439. Cells were stained for INCENP (green), plus alpha-tubulin (red) and DAPI for DNA (blue). See Fig 6A panel 1 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0x63kp1
title: CIL:12169, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. INCENP localizes to centromeres in early mitosis, but fails to transfer to the spindle midzone during late mitosis in wild type clone 18 cells grown in the Aurora B inhibitor ZM447439. Cells were stained for INCENP (green), plus alpha-tubulin (red) and DAPI for DNA (blue). See Fig 6D panel 9 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j0222sg9
title: CIL:12168, Gallus gallus gallus, memory B cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); TexasRed; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: constrained iterative deconvolution
Data qualification: Processed
description: Cell of the DT40 chicken B lymphocyte line at mitosis. Z-series of widefield immunofluorescence images captured using a 100x/1.4NA planapo objective lens on a Deltavision system and deconvolved with a constrained iterative algorithm (Applied Precision). Displayed is the central z-slice. Aurora B localizes to centromeres in early mitosis, but fails to transfer to the spindle midzone during late mitosis in wild type clone 18 cells grown in the Aurora B inhibitor ZM447439. Cells were stained for Aurora B (green), plus alpha-tubulin (red) and DAPI for DNA (blue). See Fig 6E panel 9 in Xu et al. 2009 J Cell Biol 187, 637-653.
DOI: 10.6075/j06972bc
title: CIL:41544, Homo sapiens, ciliated epithelial cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: hematoxylin; eosin
description: Histology sample illustrating the pseudostratified, ciliated columnar epithelium of the trachea. Note that the basement membrane underlying this particular epithelium is especially prominent. This image is slide 40 in the University of Michigan Histology and Virtual Learning Resource. A more detailed description can be found by following the indicated url link http://histology.med.umich.edu/medical/connective-tissue.