cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0kk99kb
title: CIL:11370, Cavia porcellus, spermatid. In Cell Image Library

description: Figure 205 from Chapter 6 (Golgi Apparatus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Sequence of the development of the acrosomal cap in spermatids from guinea pig testis, as observed in electron microscopic images. Initially, membrane-bound vesicles appear in the Golgi (A). These coalesce into larger proacrosomal granules (B), one of which attaches to the nuclear envelope (C) and the other vesicles appear to merge with the attached vesicle (D). Once attached, the acrosome further enlarges to its final volume, the Golgi apparatus leaves its surface and migrates to the caudal cytoplasm (E - G). A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned 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
Data qualification: Processed
DOI: 10.6075/j0fn151x
title: CIL:11362, Mus musculus, epithelial cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; embedded tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned 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: osmium tetroxide
Data qualification: Processed
description: Figure 199 from Chapter 6 (Golgi Apparatus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. The Golgi apparatus in epithelial cells from the mouse epididymis. The convex, or cis, side of the Golgi shows selective deposition of osmium, whereas the concave, or trans, side is resistant to osmium staining even after long periods of postosmication. Tissue shown here was prepared with collidine-buffered osmium fixation followed by 40 hours postosmication at 37° C. Image by Daniel Friend. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0s75fkw
title: CIL:1136, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 4 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: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j0dv1hpb
title: CIL:11358, Ovis aries, Cavia porcellus, spermatid, spermatocyte. In Cell Image Library

description: Figures 197 (upper) and 198 (lower) from Chapter 6 (Golgi Apparatus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. show electron microscopic views of the Golgi complex. Upper panel: A thin section preparation show the Golgi complex in the caudal cytoplasm of a ram spermatid. The cisternae are tightly packed, suggesting this organelle is relatively inactive. Lower: Freeze fracture replica of a more active Golgi complex from a guinea pig spermatocyte. Arrows point to expanded peripheral portions of the cisternae. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded tissue; freeze_fracture/freeze_etch
Relation to intact cell: microtome-sectioned 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; differences in deposition of metal shadow
Visualization methods: osmium tetroxide; shadowing and plating
Data qualification: Processed
DOI: 10.6075/j03n22qx
title: CIL:40355, Rosa rugosa, pollen. In Cell Image Library

description: Preparation: acetolysis
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: gold
Processing history: unprocessed raw data
description: Scanning electron micrograph of Rosa rugosa (Beach rose) pollen. These specimens have been acetolyzed to remove cytoplasm and pollenkit in order to reveal the intricate wall structure. This is part of a large image collection of scanning electron micrographs of pollen samples. Images of a particular species are grouped together. However, to find images and groups of images from other species, please search for the the name of the contributor, Louisa Howard.
description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
DOI: 10.6075/j03r0rj7
title: CIL:38717, Chlamydomonas reinhardtii. In Cell Image Library

description: Idolated thylakoid membranes were cryoprotected with glycerol, cryofixed, fractured at -100C, shadowed with Pt, and replicas prepared by carbon coating. Cleaned replicas were examined with a Philips 300 TEM. See Goodenough and Staehelin 1971 J Cell Biol 48:595-619
description: Preparation: cryofixed tissue; freeze_fracture/freeze_etch
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 deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
description: Isolated chloroplast membranes of the unicellular photosynthetic alga Chlamydomonas reinhardtii were cryofixed, freeze-fractured, and surface replicas observed by transmission electron microscopy. With the ac-31 mutant, and the in vitro conditions used, thylakoid membranes form stacked regions with fracture faces showing the characteristic particle sizes and distributions. See Fig 20 in Goodenough and Staehelin 1971 J Cell Biol 48:595-619.
DOI: 10.6075/j0sf2vjb
title: CIL:45752, Homo sapiens. In Cell Image Library

description: Plate 20589 - 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/j0j102b2
title: CIL:10018, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Organization of Golgi and endoplasmic reticulum (ER) in a Human HeLa cell expressing Sialyl Transferase-EGFP (green) and Invariant Chain33-mRFP (red). The Sialyl Transferase-EGFP is a Golgi marker and the Invariant Chain33-mRFP is retained in the ER. 

Zeiss Spinning Disc confocal used with with 220 ms exposure and a 63X oil objective.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: mRFP1; EGFP
Processing history: channels merged as color
DOI: 10.6075/j0kd1x1v
title: CIL:10052, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and lie parallel to the outer surface of the central nervous system, such that sections cut tangential to the membrane surface (see CIL:9301) show the spirals but transverse sections such as this one do not. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
DOI: 10.6075/j0hm58gs
title: CIL:10016, Mus musculus, early embryonic cell, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Item type: wide-field detection
Imaging mode: fluorescence microscopy; fluorescence emission; widefield illumination
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); phalloidin; Alexa Fluor 488
Processing history: charge coupled device (CCD)
DOI: 10.6075/j00z72dz
title: CIL:10013, Didinium nasutum, 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: film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: An oblique section shows the transverse aspect of basal bodies/cilia within one pectinelle of one of the two ciliary girdles of Didinium. Two ribbons of microtubules and a short kinetodesmal fiber arise from the proximal margin of each basal body. These may correspond to transverse microtubules and postciliary microtubules of other ciliates. Tips of parasomal sacs are also present. Microtubular ribbons under the alveoli seem to arise from extensions of the postciliary microtubules. TEM taken on 5/9/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:4663) is in the library and 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 thickness.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j01c1w31
title: CIL:1024, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 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: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j03x86qm
title: CIL:10117, 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
Source of contrast: distribution of epitope; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 5 days in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field.
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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 20X lens (HC PL Fluotar, NA 0.5), 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.
DOI: 10.6075/j0n29wzr
title: CIL:10135, Caenorhabditis elegans, skeletal muscle cell, oocyte, gut endothelial cell, hypodermal cell. In Cell Image Library

description: Adult Caenorhabditis elegans (C. elegans) nematode imaged by DIC (differential interference contrast) microscopy. The angle of light allows for the visualization of many of the tissues in this living transparent animal. The head is at the top of the image pointing to the left. The large cuboidal cells in the center of the animal are unfertilized oocytes. The visibly twisting tube leading down towards the tail is the gut or intestine. This animal is alive and would have likely crawled away after this image was taken.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: differential interference contrast microscopy; optical path length gradient
Source of contrast: boundaries between regions with different refractive index
DOI: 10.6075/j0wh2pz8
title: CIL:10119, Rattus, multipolar neuron. In Cell Image Library

description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 5 days in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field.
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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 20X lens (HC PL Fluotar, NA 0.5), 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
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0zw1kh7
title: CIL: 52982, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 5, z=12 from SC_011
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 image
DOI: 10.6075/j0862f21
title: CIL:47592, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP labelled S. aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue)
description: Visualization of neutrophil recruitment in capillaries proximal to S. aureus beads. (Figure 3 - Icam1)
DOI: 10.6075/j0k64grz
title: CIL:13472, Drosophila melanogaster, garland cell. In Cell Image Library

description: Transmission electron micrograph of Drosophila nephrocyte garland cell from wild type pulsed with the fluid-phase endocytic tracer HRP, detected by chromogenic staining (DAB). Most HRP-labeled endosomes in wild-type garland cells are about 100 nm in diameter. In the majority of the labeled endosomes, the HRP reaction product fills the luminal space. Third instar larvae were dissected in ice-cold PBS, equilibrated in HL-3 buffer at room temperature, incubated in 0.7% HRP (Sigma-Aldrich grade VI) for 5 min at room temperature, rinsed thoroughly, and chased for 10 min at room temperature. Samples were fixed for 1 h at 4°C in 2% paraformaldehyde, 2% glutaraldehyde, and 1% tannic acid in 0.1 M cacodylic acid buffer, pH 7.2, and processed for DAB reaction as described previously (Kosaka and Ikeda, 1983). Garland cells were dissected out and fixed for 1 h at 4°C in 2% paraformaldehyde, 2% glutaraldehyde, and 1% tannic acid in 0.1 M cacodylic acid buffer, pH 7.2. Then, the samples were postfixed in 1% OsO4 in 0.1 M cacodylic acid buffer, pH 7.2, for 1 h at room temperature, stained en bloc with 1% uranyl acetate, dehydrated in a grade series of ethanol and propylene oxide, and embedded in epon resin (Electron Microscopy Sciences). Blocks were sectioned in an ultramicrotome (RMC Products) at ∼70-nm thickness with a Delaware Diamond knife and post-stained for 1 h in Reynolds lead citrate and uranyl acetate. Electron micrographs were taken on a transmission electron microscope (H-7500; Hitachi) using an AMT camera system. Mag: 40000x. Image corresponds to Figure 4C, top panel in Kim et al. J Cell Biol. 188: 717-734. 2010.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: uranyl salt; lead salt; osmium tetroxide; horseradish peroxidase
Data qualification: Raw;intensitiesquantitation