cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0g73d9b
title: CIL: 53100, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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
description: Image 2, z=4 from SC_030
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0dv1jq6
title: CIL:36906, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #2 (day 2) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired daily over 3 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
DOI: 10.6075/j0gx4b0r
title: CIL: 51237, 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/j0fj2fp3
title: CIL:36535, Xenopus laevis, fertilized egg. In Cell Image Library

description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0nc6046
title: CIL:36470, Xenopus laevis, fertilized egg. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j0833qkd
title: CIL:46000, Homo sapiens. In Cell Image Library

description: Plate 26128 - 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/j0jq10j6
title: CIL: 52400, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=5, z=18 from BL024199_Myc_Terc
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
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j07m06mc
title: CIL:7598, Cavia porcellus, hepatocyte. In Cell Image Library

description: Pieces of liver tissue were removed directly from anesthetized animals and immersed in a drop of fixative of 1% osmium tetroxide buffered at pH 7.6 with phosphate buffer. Tissue blocks were embedded in Epon. Sections were stained with uranyl acetate and lead hydroxide. Micrograph was taken at original magnification of 65,000 X with a Siemens Elmiskop I, operating at 60 or 80 kv, with a double condenser, and a 50 µ objective aperture. Digitization process: Lantern slide scanned at 1200 dpi in TIFF format, then reduced to 600 dpi TIFF file (3500 x 3067 pixels) prior to conversion to JPEG2000 format. Original resource provided as a 3.25 x 4 inch lantern slide by George E. Palade; original is in the Palade Collection, University of California, San Diego.
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: lead salt; uranyl salt
Processing history: digitized lantern slide
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: This is a view of apical domains of two adjacent hepatocytes showing the junctional complexes that attach cells to one another. The canaliculus is defined by the cell membranes of two adjacent liver cells. At the level of the tight junctions (also known as zonula occludens) the intercellular spaces are sealed, thereby preventing leakage of bile from the canaliculus. Two adherens junctions (also known as zonula adherens) and two desmosomes are seen distal (relative to the canaliculus) to each tight junction. Glycogen particles are apparent in the cytoplasm of the liver cells. First description of tight junctions and the junctional complexes between epithelial cells from many tissues. Identical labeled image available as CIL# 7599. Image published as Figure 13 in Farquhar and Palade, 1963.
DOI: 10.6075/j0kp811h
title: CIL:25382, Maize mosaic virus, Peregrinus maidis, CNS neuron (sensu Nematoda and Protostomia). In Cell Image Library

description: Aggregates of Maize mosaic virus (MMV, Rhabdoviridae) in cells of brain of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). Antibodies to MMV identify aggregates (green/yellow fluorescence) that accumulate mainly around the nuclei (red) in this tissue.

Methods: Dissected insect organs were fixed in paraformaldehyde, labeled with primary antibodies to MMV, and with secondary antibodies: Alexa Fluor-488 (green), and later stained with the nuclear stain propidium iodide (red). Whole mounts were examined with confocal laser- scanning microscope (Leica TCS SP).

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.
description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; propidium iodide
Processing history: recorded image
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0z0371m
title: CIL:24812, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-Vps74 in BY4742 sac1∆ vps74∆. SAC1 encodes an integral membrane phosphoinositide phosphatase that is localized to the ER and Golgi. In the sac1∆ vps74∆ mutant, GFP-Vps74 localizes, in addition to the Golgi apparatus, to nuclear ER and cortical ER and/or PM as shown with colocalization of resident ER protein Sec63-mCherry (CIL# 24813). Thus, correct Golgi localization of Vps74 and GOLPH3 (see CIL#24815 for GFP-GOLPH3 in sac1∆ vps74∆ mutant) requires synthesis of PtdIns4P in the Golgi by Pik1-Frq1 and maintenance of low PtdIns4P levels in non-Golgi membranes by the Sac1 lipid phosphatase. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1B Vps74/sac1∆ panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1B include CIL#s 24815, 24812, 24813.
DOI: 10.6075/j0c8282k
title: CIL:24811, Xenopus laevis, keratocyte. In Cell Image Library

description: Localization of Xenopus ADF/cofilin (XAC) to posterior regions of depolymerization-resistant actin brush. Electron micrograph of lamellipodia of Xenopus keratocytes after latrunculin a treatment ( 0.25 μM for 10 min) and subsequent staining with XAC antibody. Image correspond to Figure 10 c from J Cell Biol. 1999 May 31;145(5):1009-26.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; polyethylene glycol
Relation to intact cell: dispersed cell 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
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).
DOI: 10.6075/j06m35q4
title: CIL:24806, Xenopus laevis, keratocyte. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; permeabilized tissue; polyethelyne glycol
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Tetramethyl rhodamine (TRITC); phalloidin
Processing history: unprocessed raw data
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 XAC (Xenopus ADF/cofilin) in Xenopus keratocytes. Fluorescence microscopy of a whole cell double stained with XAC antibody (green) and TRITC-phalloidin (red). XAC in lamellipodium is excluded from the narrow zone at the extreme leading edge. Immuno-EM with localization of XAC is shown in CIL 24807 and 24808. Image corresponds to Figure 8a-c from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6075/j0pk0fbc
title: CIL:24774, Rattus norvegicus, epithelial cell. In Cell Image Library

description: Preparation: tissue in epoxy resin embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw
description: Cells were grown on 100-mesh gold EM grids, and maintained at 15°C for 4 hours before plunge freezing in liquid nitrogen (BalTec HPM-010), followed by freeze-substitution (1% glutaraldehyde, 0.1% tannic acid in acetone, replaced with 4% osmium tetroxide and 0.01% uranyl acetate), then embedded in Epon-Araldite and sectioned at 40nm (UltraCut-UCT, Leica). Sections were transferred to formvar-coated copper-rhodium slot grids (EMS) and stained with 2% aqueous uranyl acetate and Reynold's lead citrate. Images were acquired at a magnification of 13,000X with an FEI Tecnai TF20 transmission EM. For additional details refer to: Mol Biol Cell 13:2810-2825.
description: This image is one from a set of 40nm thick serial sections through part of a Golgi ribbon from a normal rat kidney cell, generated using transmission electron microscopy following incubation at 15°C to block transport out of the Golgi complex. Following temperature block, large bulging domains appear on the three trans-most cisternae. The images in this set were used in 3-dimensional reconstructions of the Golgi apparatus. For more information see: Ladinsky et al. (2002) Structure of the Golgi and distribution of reporter molecules at 20°C reveals the complexity of the exit compartments, Mol Biol Cell 13:2810-2825. The other images from this serial set are included in this image group.
DOI: 10.6075/j0f76bp8
title: CIL:24773, Rattus norvegicus, epithelial cell. In Cell Image Library

description: This image is one from a set of 40nm thick serial sections through part of a Golgi ribbon from a normal rat kidney cell, generated using transmission electron microscopy following incubation at 15°C to block transport out of the Golgi complex. Following temperature block, large bulging domains appear on the three trans-most cisternae. The images in this set were used in 3-dimensional reconstructions of the Golgi apparatus. For more information see: Ladinsky et al. (2002) Structure of the Golgi and distribution of reporter molecules at 20°C reveals the complexity of the exit compartments, Mol Biol Cell 13:2810-2825. The other images from this serial set are included in this image group.
description: Cells were grown on 100-mesh gold EM grids, and maintained at 15°C for 4 hours before plunge freezing in liquid nitrogen (BalTec HPM-010), followed by freeze-substitution (1% glutaraldehyde, 0.1% tannic acid in acetone, replaced with 4% osmium tetroxide and 0.01% uranyl acetate), then embedded in Epon-Araldite and sectioned at 40nm (UltraCut-UCT, Leica). Sections were transferred to formvar-coated copper-rhodium slot grids (EMS) and stained with 2% aqueous uranyl acetate and Reynold's lead citrate. Images were acquired at a magnification of 13,000X with an FEI Tecnai TF20 transmission EM. For additional details refer to: Mol Biol Cell 13:2810-2825.
description: Preparation: tissue in epoxy resin embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j07m0732
title: CIL:24769, Rattus norvegicus, epithelial cell. In Cell Image Library

description: Cells were grown on 100-mesh gold EM grids, and maintained at 15°C for 4 hours before plunge freezing in liquid nitrogen (BalTec HPM-010), followed by freeze-substitution (1% glutaraldehyde, 0.1% tannic acid in acetone, replaced with 4% osmium tetroxide and 0.01% uranyl acetate), then embedded in Epon-Araldite and sectioned at 40nm (UltraCut-UCT, Leica). Sections were transferred to formvar-coated copper-rhodium slot grids (EMS) and stained with 2% aqueous uranyl acetate and Reynold's lead citrate. Images were acquired at a magnification of 13,000X with an FEI Tecnai TF20 transmission EM. For additional details refer to: Mol Biol Cell 13:2810-2825.
description: This image is one from a set of 40nm thick serial sections through part of a Golgi ribbon from a normal rat kidney cell, generated using transmission electron microscopy following incubation at 15°C to block transport out of the Golgi complex. Following temperature block, large bulging domains appear on the three trans-most cisternae. The images in this set were used in 3-dimensional reconstructions of the Golgi apparatus. For more information see: Ladinsky et al. (2002) Structure of the Golgi and distribution of reporter molecules at 20°C reveals the complexity of the exit compartments, Mol Biol Cell 13:2810-2825. The other images from this serial set are included in this image group.
description: Preparation: tissue in epoxy resin embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw