cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09c6w2z
title: CIL:34900. In Cell Image Library

description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: shadowing and plating; platinum replica
Processing history: unprocessed raw data
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Improved visualization of actin filament branching in lamellipodia. EM of keratocyte or fibroblast lamellipodial actin network after cytochalasin D treatment (0.2 μM for 30 min or 0.5 μM for 10 min). Image corresponds to a panel in Figure 2b from J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 2b are available as CIL 34894-34901.
DOI: 10.6075/j00r9p4h
title: CIL: 54254, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TKL 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: 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/j01c1w9q
title: CIL: 51314, 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: 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: ~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/j0bc3xjt
title: CIL:7417, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: Pixel value determine by specimen height
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2, which appears as bright circles in AFM images, and volume measurements of the complexes suggest that MeCP2 monomers and dimers are present and that MeCP2 binds DNA cooperatively. Other images in the linked set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2.
DOI: 10.6075/j0s46qpw
title: CIL:11971, Spisula solidissima, oocyte, zygote. In Cell Image Library

description: K Dan and S Inoue 1987 Studies of unequal cleavage in molluscs: asymmetric nature of the two asters. Int J Invert Rep Dev 11:335-354.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: polarization microscopy
Parameter imaged: retardance
Source of contrast: form birefringence
Visualization methods: visualization of contiguous regions
Data qualification: Processed
description: The time lapse movie shows the rocking motion of the spindle that appears to play a role in the unequal cleavage divisions in a fertilized Spisula solidissima (Clam) egg. Eventually, this leads to the production of three small cells and one large.
DOI: 10.6075/j0df6qz5
title: CIL: 54156. 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: TK 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
DOI: 10.6075/j09p31pn
title: CIL:2939, Rattus, multipolar neuron. In Cell Image Library

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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: Development of the axon and dendritic arbors in cultured hippocampal neurons after 3 days in vitro. MAP2 staining (red) highlights the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Neurons at 2, 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), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 20X (Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Image generated with the MetaMorph color combine function.
DOI: 10.6075/j0v40tqx
title: CIL: 52195, 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: 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.
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.
DOI: 10.6075/j0cj8c4r
title: CIL:31262, Homo sapiens, epithelial cell, renal cell carcinoma. In Cell Image Library

description: RCC-4 cell stained with anti-alpha-tubulin (green) and anti-GTP-tubulin (red) antibodies. GTP-tubulin localizes to the microtubule (MT) tip and remnants of GTP-tubulin are found along the entire MT lattice. RCC-4 cells lack Von Hippel-Lindau (VHL) and when pVHL30 is expressed in these cells, a higher frequency of GTP caps and GTP remnants is observed. RCC-4 cells were permeabilized in PEM buffer with glycerol and 0.1% Triton-X100, then incubated with primary antibody hMB11 followed by incubation with secondary antibody. Cells were then fixed in cold methanol for 5 min and stained with the polyclonal anti-tubulin antibody followed by secondary antibody. Stacks of images were acquired with an IX70 Delta Vision Spectris microscope using a 60X NA1.4 DIC oil Plan-Apochromat objective. This stack corresponds to J Cell Biol. 2010. 190: 991-1003--control Fig 5F (left 2 panels) and the experimental with ectopic pVHL30 (right 2 panels in Fig 5F) is CIL# 26572.
description: Preparation: methanol fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j09w0fk6
title: CIL:35812, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged MCM1. 
 
 MCM1 is a transcription factor involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes
 
These phase,gfp images are part of an image group that ranges from CIL:35880-35899. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the 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
DOI: 10.6075/j0g73crr
title: CIL:7748, Nassula, 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;intensitiesquantitation
description: A high resolution image of the endoplasmic reticulum that exists in extensive sheets in the cytoplasm of Nassula immediately below the alveolar membranes. TEM taken on 3/14/69 by R. Allen with Philips 300 operating at 60kV. Neg. 16,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available 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.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0ht2pgp
title: CIL:40131, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: The neostriatum of a transgenic mouse engineered to overexpress a mutant form of human alpha synuclein (A53T), immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
DOI: 10.6075/j0zs2vvc
title: CIL:45759, Homo sapiens. In Cell Image Library

description: Plate 20596 - 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/j0nz86k4
title: CIL:36646, 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; uranyl salt; lead salt; osmium tetroxide
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. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: The macronucleus is the largest organelle in the P. multimicronucleatum cell and can measure 35µm long by 12µm wide. A small fraction of a macronucleus is seen in this micrograph. The chromatin appears as thousands of small electron opaque foci scattered throughout a moderately stained nucleoplasm. In addition this nucleus contains numerous larger electron-opaque nucleoli scattered equally through the nucleoplasm. Nucleoli are sites of ribosome subunit synthesis. This cell was in day 1 of the culture age study and the cell had large regions of rough ER that were covered with large numbers of ribosomes. There were many folds in the macronuclear surface. The nuclear envelope is packed with nuclear pores. TEM taken on 5/29/78 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 10,000X. Bar = 0.5µm.
DOI: 10.6075/j0668ctq
title: CIL: 53291, Homo sapiens, Anucleated structure. In Cell Image Library

description: Intra-alveolar amylacea body, CD31+ peripheral membrane, adherennt CD31+ monocyte/macrophage
description: CD31 immunohistochemsitry
description: Imaging mode: recorded image
Visualization methods: microscopy