cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0sx6c0q
title: CIL:41695, Homo sapiens, osteocarcinoma. In Cell Image Library

description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met: The publication and/or presentation are solely for informational and non-commercial purposes. The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody 
 HPA041411 (shown in green). HPA041411 is a polyclonal anti-SSRRM2 antibody that labels the nucleus but not the nuclei. The cells are also stained with a reference marker in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probe/organelle was used as references; anti-tubulin antibody as internal control and marker of microtubules (red).
DOI: 10.6075/j0jq1075
title: CIL:2240, 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 6 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/j0t72gxz
title: CIL: 51983, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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.
DOI: 10.6075/j0c24vjk
title: CIL:9853, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The radial arms of the Contractile Vacuole Complex or CVC each contain a collecting canal enclosed by a microtubular ribbon split lengthwise into several smaller ribbons, a meshwork of smooth spongiome and, peripheral to this, the bundles of tubules of the decorated spongiome. The microtubules along the collecting canal are immunogold-labeled with anti-b-tubulin as are some single microtubules in the area. TEM taken on 7/8/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 7,900X. Bar = 1µm. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:36689) is in the library and available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0v123gt
title: CIL:13589, Mus musculus, myoblast. In Cell Image Library

description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The myoblasts in this image were untreated during differentiation. 
This image is the control of different treatments in Figure 9A from JCB 189: 1157-1169, 2010. See also CIL: 13590, 13591.
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0cn72j2
title: CIL:38859, Arabidopsis thaliana, leaf. In Cell Image Library

description: Leaves from wildtype Arabidopsis thaliana were fixed, embedded, sectioned, reacted with antibodies to the FtsZ1-1 protein (upper panels) or FtsZ-2 (lower panels), prokaryotic cell division proteins that are a structural homolog of tubulin. The protein is localized at the site of division which occurs by constricting at the chloroplast mid-point. Shown (from left to right) are focal planes from the bottom, middle and top of the chloroplast, with the projection image at far right revealing the ring-shaped FtsZ distribution.
description: Leaves were fixed in FAA (formalin acetic acid), embedded in low melting point polyester wax, and 7 micrometer sections cut and attached to poly-L-lysine slides. Sections were de-waxed, treated with an antigen retrieval procedure, and processed for immunofluorescence using incubation with an affinity purified polyclonal antibody, followed by FITC-conjugated secondary antibody. Slides were viewed with an Olympus BH2 microscope equipped with DIC optics. Images were recorded on film, or a video camera (Optronics DEI 750 using a 100x 1.25 NA objective lens. Shown are 3 focal planes. To generate the 3D image shown at far right the z-stack was rotated 30 degrees and projected. See S. Vitha et al. 2001 J Cell Biol 153:111-119.
description: Preparation: formaldehyde fixed tissue; tissue in wax embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Fluorescein (FITC)
Data qualification: Processed
DOI: 10.6075/j08k78fk
title: CIL:40358, Rattus norvegicus, oligodendrocyte. In Cell Image Library

description: Rattus norvegicus oligodendrocytes purified from P2 cortex. Cells were fixed on glass coverslips with 4% PFA and immunostained with Phalloidin-FITC (green), alpha-tubulin primary ab./Rhodamine secondary ab (red), RIP (oligodendrocyte marker) primary ab/Cy5 secondary ab (blue), and DAPI (nuclear marker also in blue). Photographed using Leica DMI4000B microscope and 63x HCX PL APO OIL Objective. Voxel size 0.1um.
description: Preparation: formaldehyde fixed tissue
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: phalloidin; primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
description: This fluorescent micrograph is part of an image group displaying the morphological changes associated with a developing oligodendrocyte. The progression of images starts with CIL:40358 where cells display a relatively bipolar morphology to CIL:40359 where the actin cytoskeleton becomes very prominent to CIL:40360 where the actin coalesces and interlinks, and finally there is CIL:40361 where one can observe the formation of a flattened lamellar structure which in vitro mimics the myelin sheet.
DOI: 10.6075/j0dr2tvn
title: CIL: 50719, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 5.7_Cell_5_MATLAB_Volume_Analysis_Results. In Cell Image Library

description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Mictoscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
5.7_Cell_5_MATLAB_Volume_Analysis_Results is a compressed (zipped) folder containing all files required to execute the MATLAB volume analysis. The folder also includes the resulting output files and figures.
This file is a part of Dataset 5, comprised of files related to the Cell #5 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
DOI: 10.6075/j0x63mgr
title: CIL: 52552, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=4, y=4, z=2 from BL32080_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
DOI: 10.6075/j07d2tjm
title: CIL:45901, Homo sapiens. In Cell Image Library

description: Plate 25679 - 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/j0w0956p
title: CIL:257, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
description: Thin section electron microscopy of diaphragm (skeletal) muscle from a wild type mouse.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 30,000X magnification.

This image is part of a set of wild type diaphragm muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
DOI: 10.6075/j0w9582q
title: CIL:25694, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Time lapse series of cell growth and division in cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) using phase contrast optics. A movie created from this time series is grouped with it in the Cell Image Library.
description: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica 40x HCX PL APO NA 1.25 objective lens. images were captured at 3 minute intervals with a Hamamatsu ORCA-ER2 CCD camera using Simple PCI 6.6.0.0 software.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0x0664c
title: CIL:2571, 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 10 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/j0tx3dbs
title: CIL:25709, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Time lapse series of cell growth and division in cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) using differential interference contrast optics. A movie prepared from the time series is grouped in the Cell Image Library.
description: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica HCX PLAN APO 100x NA 1.35 DIC objective lens. images were captured at 30 second intervals with a Hamamatsu ORCA-ER2 CCD camera using Simple PCI 6.6.0.0 software.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
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
DOI: 10.6075/j0f76b9b
title: CIL:25703, Rattus, mammary adenocarcinoma. In Cell Image Library

description: Preparation: living tissue
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 a specific protein
Visualization methods: EYFP
Processing history: watershed filtering
description: MTLn3 cell cotransfected with control siRNA and two tandem Src SH2 phosphotyrosine-binding domains (YFP-dSH2), which specifically detects tyrosine phosphorylation at focal adhesions. CIL:25702 is corresponds to FAK siRNA (target A). Fluorescence imaging was performed using a 60×/1.40 oil objective on an inverted microscope (1X-70;Olympus) in a 37°C closed system as previously described. Glass-bottomed dishes (35 mm) were coated with 10 µg/ml fibronectin for 1 h at 37°C. Cells were plated in Ham's F12 containing 5% FBS and 20 mM Hepes, pH 7.2, and were allowed to adhere for 3 h. Fluorescent images were collected using a cooled CCD camera (CoolSNAP FX; Hamamatsu Photonics) and captured into MetaVue every 1 min for 1 h. Time-lapse sequences from live fluorescence imaging were first subjected to high-pass filtration based on the water algorithm (Zamir et al., 1999) to remove diffuse background fluorescence. Movie corresponds to video 4 from J Cell Biol. 2009 Apr 20;185(2):357-70. Epub 2009 Apr 13.
DOI: 10.6075/j03t9g2r
title: CIL:25701. In Cell Image Library

description: Time-lapse TIRF visualization of GFP-tagged EB1 showed bright foci of EB1-GFP moving away from microtubule seeds locations corresponding to the growing microtubule ends, confirming that EB1-GFP is capable of tip-tracking growing microtubule ends without the need of any protein binding partners. Tip-tracking was observed at both the plus and minus ends of growing microtubules, but no end localization was seen for microtubules that were not growing. Bright EB1-GFP foci were not observed at the microtubule ends during periods of microtubule depolymerization. The above findings confirm previous results that the tip-tracking of EB1 relies on the process of microtubule growth. Images were taken at 5 second intervals. Microtubules were (red, imaged by EPI fluorescence) with 24 µM unlabeled tubulin, 50 nM EB1-GFP (green, imaged by TIRF) in Imaging Buffer (see Methods in corresponding paper) with additional 60 mM KCl. Video-playback is 50× times real time. Area size is 45 µmx31 µm. Video corresponds to supplemental video 1 in PLoS One. 2009 Oct 23;4(10):e7585.
description: Preparation: in vitro protein assembly
Relation to intact cell: motility reconstituted in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; TIRF
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; Rhodamine
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation