cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j08s4ppm
title: CIL: 54339. In Cell Image Library

description: CAMK 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
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.
DOI: 10.6075/j0p26z8s
title: CIL:40012, Caulobacter crescentus CB15. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; cryofixed 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
Processing history: recorded image
Data qualification: Processed
description: Image from the reconstructed volume of a Caulobacter Crescentus specimen. This particular image was taken from Z-slice #307. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Caulobacter cultures (strain NA1000) were cryofixed using rapid freezing procedures. Film images were acquired using a JEOL 4000, at a magnification of 30,000X, 400.0 Kv.
DOI: 10.6075/j0pv6kjr
title: CIL: 54849, Danio rerio, Whole larva. In Cell Image Library

description: Larvae preparation for GFP+ CLEM (eLife: Workflow #2). To facilitate the 3D correlation between different imaging modalities when using any GFP+ transgenic line, we added DRAQ5, a nuclear DNA binding fluorescent dye. Briefly, the 5 dpf transgenic zebrafish larvae were fixed with 0.5% glutaraldehyde and 2% paraformaldehyde in 0.15M cacodylate buffer (CB, pH 7.4) for 2.5 hours and 100 m thick sagittal sections were collected and incubated in DRAQ5 (1:1000, Cell Signaling Technology) on ice for an hour. Confocal images of GFP and DRAQ5 signals were collected on a Leica SPE II confocal microscope with a 20X oil-immersion objective lens using 488 nm and 633 nm excitation. Following, the samples were preincubated in 2.5 mM DAB solution (25.24 mM stock in 0.1 M HCl) in 0.15 M CB for 30 min on ice. Next, the photo-oxidation of DAB by DRAQ5 was done in 2.5 mM DAB in 0.15 M CB using a solar simulator (Spectra-Physics 92191–1000 solar simulator with 1600 W mercury arc lamp and two Spectra-Physics SP66239–3767 dichroic mirrors to remove infrared and ultraviolet wavelengths), while bubbling oxygen in the solution. The light was filtered through a 10 cm square bandpass filters (Chroma Technology Corp.) for illumination at 615 nm (40 nm band pass). The reaction was monitored every 20 minutes and stopped when the desired darkening in the nuclei was achieved. Larvae were then washed 5 times with 0.15 M CB and incubated in 2% OsO4/1.5% potassium ferrocyanide in 0.15 M CB containing 2 mM CaCl2 to get an EM visible stain. The larvae were left for 30 min on ice and then 30 min at room temperature (RT). After thorough washing in double distilled water (ddH2O), larvae were placed into 0.05% thiocarbohydrazide for 30 min. Larvae were again washed and then stained with 2% aqueous OsO4 for 30 min. Larvae were washed and then placed into 2% aqueous uranyl acetate overnight at 4°C. Larvae were washed with ddH2O at RT and then stained with 0.05% en-bloc lead aspartate for 30 min at 60°C. Larvae were washed with ddH2O and then dehydrated on ice in 50%, 70%, 90%, 100%, 100% ethanol solutions for 10 min at each step. Larvae were then washed twice with dry acetone and placed into 50:50 Durcupan ACM:acetone overnight. Larvae were transferred to 100% Durcupan resin overnight. Larvae were then flat embedded between glass slides coated with mould-release compound and left in an oven at 60°C for 72 h. The larva block was imaged with a Merlin scanning electron microscope equipped with a 3View2XP and OnPoint backscatter detector. The volume was collected at 3 kV, with 10.8 nm pixels x and y ; 70 nm Z steps and 70% local gas injection. The raster size was 25k x 12k and the volume was aligned using cross correlation and visualized using IMOD.
description: Imaging mode: SBEM
description: Sagittal sections of 5 days post-fertilization cd41:gfp+ zebrafish larva in the region of the anterior kidney (eLife Table 1: cd41:GFP 5 dpf).
DOI: 10.6075/j0j67h0b
title: CIL:32102, 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: 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
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.
DOI: 10.6075/j0n58ktw
title: CIL: 51670, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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.
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.
DOI: 10.6075/j0j1038k
title: CIL:39581, Saccharomyces cerevisiae. In Cell Image Library

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: 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; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Lte1. 
 
 LTE1 is essential for termination of M phase at low temperatures, along with TEM1, and CDC15, all part of the mitotic exit network which is an elaborate signaling system comprising at least eight essential genes: CDC5, CDC14, CDC15, DBF2, DBF20, LTE1, MOB1, and TEM1. LTE1 was originally discovered as a locus essential for growth at 8 C, and was named for this trait as Low Temperature Essential 1. It was later inferred from sequence similarities that LTE1 must code for a guanine nucleotide exchange factor. Genetic evidence suggests that Lte1p activates the GTPase Tem1p which activates the protein kinase Cdc15p. Cdc15p then relieves the inhibition of the protein phosphatase Cdc14p by Net1p, thereby allowing exit from mitosis. In a normal cell cycle, Bub2p bound to Tem1p restrains mitotic exit until the daughter-bound centrosome (with which both Bub2p and Tem1p preferentially associate) comes into contact with Lte1p in the bud, effectively coupling mitotic exit with nuclear segregation. Some evidence suggests that the spatial separation of Tem1p and Lte1p is a key mechanism for controlling the timing of mitotic exit.
 
These phase,gfp z-series images are part of an image group that ranges from CIL:39581-39585. 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/j0251hvk
title: CIL: 53355, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of Fruit Fly embryonic development. Each video is labeled with the temperature (Celcius) at which it was captured as well as the embryo name (A, B, etc)
DOI: 10.6075/j0rb7386
title: CIL:34750, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: One parasomal sac lies anterior to each basal body of the somatic ciliature. A parasomal sac is an indentation of the plasma membrane that penetrates into the cytosol past the alveolus. Most sacs end as a coated pit. However, as seen in this micrograph, they can also give rise to more extensive tubules and vesicles. These vesicles pinch off into the cytosol to become early endosomes in a process called endocytosis where they lose their coat and fuse with a flattened smooth-membraned cisterna that is the early endosome. lip, lipid droplet. TEM taken on 7/17/67 by R. Allen with Philips 200 operating at 60kV. Neg. 9,000X. Bar = 0.5µm. 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:34742) 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
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j09w0fjr
title: CIL:10273, Rattus, multipolar neuron. In Cell Image Library

description: Early stages of dendritic development and synapse formation in cultured hippocampal neurons. This multilayer image shows neurons fixed at 7 days in vitro and immunostained for the dendritically localized protein MAP2 (green) and the presynaptic vesicle protein Synapsin I (red). Unstained axons in the field are evident in the phase channel, which is hidden but can be turned on in the viewer. Neurons at 3, 5 and 7 days in vitro are represented in this image group. 

Detailed methods: 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, warmed to 37°C prior to fixation, 15 minutes), permeabilized with 0.25% Triton (7 minutes) 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 mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500; suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j06q1wmr
title: CIL:39549, 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; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: This is a time lapse image series of Saccharomyces cerevisiae expressing GFP tagged Bub2, a GTPase activator involves in mitotic cell cycle spindle orientation checkpoint and regulation of exit from mitosis. These phase and GFP z-series images are part of an image group containing CIL 39546-39550. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Images were acquired using a 60x 1.42 NA objective lens on a Delta Vision system equipped with a CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j0q52nxd
title: CIL:808, Rattus, multipolar neuron. In Cell Image Library

description: During hippocampal neuron development in vitro, N-cadherin becomes selectively localized to excitatory synapses. This image shows immunolocalization of the NMDA receptor, which is postsynaptic. Other images in this image group show immunolocalization of N-cadherin, colocalized at synapses that are also immunopositive for the presynaptic glutamate transporters V-glut 1 and 2. 
 
Individual fluorescent images were acquired using a Nikon Diaphot 300 with a 60X objective. Preparation was fixed in 4% paraformaldehyde and permeabilized with .01% TritonX-100.
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
DOI: 10.6075/j0nc60k1
title: CIL:45875, 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 25584 - 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/j0c53jh2
title: CIL:39125, Arabidopsis thaliana, leaf. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
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: uranyl salt; lead salt
Data qualification: Processed
description: 3-week old leaf tissue from Arabidopsis thaliana (eco-type Columbia - Col-0) was fixed, embedded in resin, and 70 nm serial sections cut, stained, and observed by transmission EM. See Fig 2 in H Gao et al, 2006. Proc Natl Acad Sci USA 103:6759-6764.
description: Thin section of a wildtype chloroplast of Arabidopsis thaliana showing the characteristic distribution of thylakoids membranes in stacked grana (black arrow) and unstacked stromal regions (white arrows). The other image in this group (CIL 39126) shows the result of deleting the FZL protein.
DOI: 10.6075/j0n29vtj
title: CIL:40663, Rattus, hippocampal neuron. In Cell Image Library

description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: grey scale graphic
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: colorized
description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
description: Platinum replica depicting the cytoskeletal organization of dendritic spines in extracted 14 DIV neurons. This image shows branched actin filaments (cyan) at the neck‚Äìhead junction. Dashed arrows indicate potential filament breakage. Image corresponds to Figure 2a in Mol Biol Cell. 2010 Jan 1;21(1):165-76. The entire panel is available as CIL 40660. The uncolorized image is available as CIL 40659. Box 1, 2, and 3 (this image) are CIL 40661, 40662, and 40663, respectively.
DOI: 10.6075/j0mc8z1w
title: CIL:2697, Caenorhabditis elegans. In Cell Image Library

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 8 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