cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0ww7g8h
title: CIL:37128, Rattus, endothelial cell. In Cell Image Library

description: Reference:
Simeonescu, N., M. Simeonescu, and G. E. Palade. 1975. J. Cell Biol. 64:586-607.
Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification x160,000.
description: Transmission electron micrograph of rat tongue continuous endothelium showing fused caveolae. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: 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: osmium tetroxide
DOI: 10.6075/j0tx3dvh
title: CIL: 51831, 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/j0z60nrx
title: CIL: 54462, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: hematoxylin and eosin
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for hematoxylin and eosin.
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
DOI: 10.6075/j0z60mn5
title: CIL:47580, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Mac1)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
DOI: 10.6075/j0zk5gq3
title: CIL:36175, Rattus, multipolar neuron. In Cell Image Library

description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density of presynaptic contacts along the dendritic arbor.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
DOI: 10.6075/j0pr7v6x
title: CIL:1790, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 2 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j05q4tpn
title: CIL:46267, 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 26670 - 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/j02b8z4x
title: CIL:40000, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with either 5% aqueous LY in 200 mM KCl. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were then ready to be immunolabeled. The rabbit anti-EphA4 antibody was provided by Dr. Elena Pasquale (The Burnham Institute, La Jolla, CA). EphA4 was subsequently detected using goat anti-rabbit Cy5. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling; distribution of epitope
Visualization methods: lucifer yellow; primary antibody plus labeled secondary antibody; Cy5
Data qualification: Processed
DOI: 10.6075/j00864dh
title: CIL:11857, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0m61jfx
title: CIL:11856, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j01v5d3k
title: CIL:11855, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j0vm4bfw
title: CIL:11854, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j00g3k5p
title: CIL:35620, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; differences in amount of elastic light scattering
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cln2. Cln2 is a G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p).These phase,gfp images are part of an image group that ranges from CIL:35620-35639. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.6075/j0k936mh
title: CIL:24484, 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 250nm (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. Digital images were acquired at a magnification of 15,000X with an FEI Tecnai TF20 transmission EM. For additional details refer to: J. Cell Biol. 144 (6) 1135-1149.
description: This image is from a tomogram through part of a Golgi ribbon from a normal rat kidney cell, generated using high voltage 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 sample was tilted at angles of 1.5° to obtain the series of images in this set, and used to obtain 3-dimensional reconstructions of the Golgi apparatus and contributed to findings reported in Ladinsky et al. (1999) Golgi structure in three dimensions: Functional insights from the normal rat kidney cell. J. Cell Biol. 144 (6) 1135-1149.
description: Preparation: tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
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/j0cf9q3s
title: CIL:32087, Homo sapiens, osteocarcenoma. In Cell Image Library

description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j098867n
title: CIL:1756, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 2 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0np2430
title: CIL: 53618, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Atypical family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy