cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0736psh
title: CIL:36536, 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/j0pc31tr
title: CIL: 50931, Human mast cell line (HMC-1), Human mast cells. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Human mast cell line 1 (HMC-1) were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
DOI: 10.6075/j0445krv
title: CIL:556, Acetabularia mediterranea, gamete. In Cell Image Library

description: At cyst formation in the 'giant' unicellular green alga Acetabularia, each cyst contains a single nucleus which subsequently undergoes several rounds of mitosis prior to gamete formation. Initially the nuclei form a syncytium which separates into individual gametes. This section shows a stage in gametogenesis where the syncytium has just started to divide into uninuclear gametes, and the formation of flagella from paired centrioles is in progress. See Woodcock and Miller, 1973. Ultrastructural features of the life cycle of Acetabularia I Gametogenesis. Proptoplasma 77, 313-319.
description: Cysts were fixed in glutaraldehyde, post-fixed in osmium tetroxide, epoxy embedded, and thin sections stained with aqueous uranyl acetate and lead citrate. Grids were examined with a Philips 400 TEM operated at 80KV and images recorded on film.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: unprocessed raw data
DOI: 10.6075/j0154fzx
title: CIL:35127, Mus musculus, macrophage. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
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
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Primary bone marrow macrophages derived from mouse plated on a coverslip and imaged live. Phase contrast microscopy allows us to see the dense f-actin rich leading edge, ruffles, mitochondria, the nucleus, and other organelles throughout the volume of the cells. At the center of the image is a polarized lamellipod of a crawling cell. The glass micropipette at the bottom of the image is delivering CSF (colony stimulating factor) locally and the cell may be responding.
description: Live bone marrow macrophages plated in MatTek dish and imaged with a 60X N.A. 1.4 phase 3 Olympus objective on an IX71 microscope with a Cooke Sensicam QE camera and IPLab software running on a Dell Windows XP computer.
DOI: 10.6075/j0sj1j8p
title: CIL:13438, Homo sapiens, breast. In Cell Image Library

description: FISH detection of ERBB2 (fluorescein, green) and MYC (rhodamine, red) in normal breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Z-stacks were acquired to cover the thickness of the tissue section with a step size of 0.5 microns in the Z-direction, and subjected to deconvolution using SoftWoRx 3.5.1 software. A maximum intensity projection of the stack is shown. The complete stack is included in this group of images.
 A portion of this field of view is shown in Fig 1B of Meaburn et al., 2009, J Cell Biol 187:801-812.
description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j01v5djd
title: CIL: 52757, 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: One z layer of a z-stack at the given tile position
description: Tile x=4, y=4, z=18 from PS11_10021_2B_Myc_Terc
DOI: 10.6075/j0d50n2n
title: CIL:40256, Rattus norvegicus, peripheral neuron. In Cell Image Library

description: Chemical fixation with 2% paraformaldehyde and 2.5% glutaraldehyde via vascular perfusion in 0.15M cacodylate buffer (pH 7.4) at 37 degrees C followed by high pressure freezing and freeze substitution using a Bal Tec HPM010 high pressure freezer (from Perkins et al., J. Structural Biology 161, 469, 2008).
description: Single computed slice through a tomographic volume of mitochondria at the Node of Ranvier in rat peripheral nerve root. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Perkins et al. Mitochondrial configurations in peripheral nerve suggest differential ATP production. J. Struct. Biol. (2010), doi:10.1016/j.jsb.2010.06.017 http://www.ncbi.nlm.nih.gov/pubmed/20600951
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
DOI: 10.6075/j0k0743c
title: CIL:37056, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

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 #4 (6 hours) of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 Complete z-stacks were acquired of this neuron at a 2 hour interval over 8 hours. These images are part of this image group. This time lapse series shows the development of the neuron's dendritic arbor. The dendritic arbor exhibits morphological plasticity with branch additions, retractions and extensions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the 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.
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: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0ht2n57
title: CIL:39471, Ascidiacea, embryonic cell. In Cell Image Library

description: Early ascidian (sea squirt) embryos visualized by differential interface contrast (DIC) microscopy. Ascidians are used as a model for developmental research. Their simple embryonic development is rapid and can be easily manipulated. In addition, each embryo contains only a few cells therefore complex cellular processes can be studied while remaining part of an intact embryo. The embryos are also transparent, which is ideal for fluorescent microscopy thus allowing scientists to visualize different developmental stages. A lower magnification image is available as CIL:39466.
description: B0008314 Ascidian embryo. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
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
DOI: 10.6075/j0kp80vv
title: CIL:13753, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 a specific protein; compartmentalization of stain or label
Visualization methods: primary antibody plus labeled secondary antibody; membrane-permeant probe; EGFP; DRAQ5
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Expression of UAS-tauGFP (the tau-GFP fusion protein binds microtubules; green) under control of 109-30-Gal4 in wild-type Drosophila germaria. 109-30-Gal4 drives UAS-tauGFP expression in follicle stem cells and their progeny cells (see also CIL# 13752). Nuclei are in red. Image correlates to Supplemental Figure S2C in J Cell Biol. 2010. 191: 943-952.
description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). Primary antibody was anti-GFP. Secondary antibodies used were either FITC, Cy3, or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). For nuclear staining, fixed ovaries were incubated for 15 min with Draq5 (Cell Signaling Technology). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
DOI: 10.6075/j0tt4qf6
title: CIL: 52051, Homo sapiens. In Cell Image Library

description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
DOI: 10.6075/j0df6qgw
title: CIL:767, Patiria miniata, sperm. In Cell Image Library

description: Phosphorus has a characteristic electron energy loss with an edge at 160 eV. The Zeiss 902 electron microscope permits images to be recorded at different energy losses which can be digitized and processed to yield a net phosphorus image. For nuclear chromatin, phosphorus is primarily located in DNA, allowing its distribution in chromatin fibers to be mapped. Electron energy loss (EELS) imaging is also known as electron spectroscopic imaging (ESI) and electron energy filtering TEM (EFTEM).
Starfish sperm chromatin, which has clearly defined chromatin fibers was fixed, embedded in Lowicryl at low temperature, thin sections prepared and imaged unstained. The 4 grouped images were recorded with a Zeiss 902 energy filtered TEM at 80KV using 5eV windows centered on energy loss values of 170, 160, 120, and 104eV (this image).
description: Preparation: glutaraldehyde fixed tissue; Low temperature embedding
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: modes of electron microscopy; EELS imaging
Source of contrast: electron scattering
Visualization methods: EELS window
Processing history: unprocessed raw data
DOI: 10.6075/j0w094mn
title: CIL:13763, Rattus norvegicus, pheochromocytoma, adrenal gland cell. In Cell Image Library

description: Electron micrograph of PC12 cells transfected with AP-3 siRNA. PC12 cells were plated onto aclar film discs (Pella) coated with poly-L-lysine, transfected twice with 50 nM AP-3delta1 siRNA and fixed with 2.5% glutaraldehyde in calcium-/magnesium-free PBS. The discs were washed three times with 0.1 M sodium cacodylate buffer, pH 7.2, and postfixed for 30 min on ice with 1% osmium tetroxide in cacodylate buffer containing 1.6% potassium ferricyanide. The discs were then washed three times with cacodylate buffer, three times with water, incubated with 0.5% uranyl acetate for 30 min (in the dark), and washed again with water. The samples were dehydrated in a graded series of ethanols while progressively lowering the temperature from 4°C to −40°C then embedded in epon resin. After peeling off the aclar, 60-nm sections were cut and viewed in an electron microscope (FEI Tecnai 12; Phillips) at 120 kV, images were captured with a digital camera at 6,800 magnification. Image is similar to Fig 6C right panel (CIL# 13764) of J Cell Biol. 2010. 191: 1173-1187.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: cryostat-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0cz3695
title: CIL:12068, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
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: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image. Basal bodies are supported by three fiber systems, a striated kinetodesmal fiber that arises from the proximal end of the basal body and curves upward and anteriorly within the longitudinal ridge to the cell's right side of a row of basal bodies. Extending posteriorly and also curving up into the longitudinal ridge is a ribbon of postciliary microtubules. The kd may extend past several more anterior basal bodies but the postciliary ribbon does not extend beyond the next posterior basal body or pair of basal bodies in the kinety. Only the more posterior of the two basal bodies within a single depression is associated with the ends of these two accessory structures. An indentation of the plasma membrane, the parasomal sac, lies to the cell's right of each basal body or pair of basal bodies. TEM taken on 1/5/73 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. 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/j0z60nfw
title: CIL:45824, Homo sapiens. In Cell Image Library

description: Plate 24795 - 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/j0f47n5m
title: CIL:6258, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6267.