cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0th8ksf
title: CIL:13150, Micrasterias denticulata. In Cell Image Library

description: Micrograph illustrating the general preservation of the cytoplasm in a Micrasterias cell stabilized by ultrarapid freezing. E-face of RER membranes depicting several spiral imprints of polysomes. The substructure of the imprint ridge presumably reflects imprints of the individual ribosomes. 

Technical details:
Cultures of Micrasterias denticulata were obtained from the Algal Culture Collection, University of Indiana (Cat. No . LB558) . Cells were grown in Waris medium MS at 18°C on a 15/9-h, fight-dark cycle. For each experiment, cells about halfway through the dark cycle were placed in fresh medium in continuous light. This treatment stimulated many cells to divide ~25 h later. Healthy, growing cells were then selected with a dissecting microscope and placed in a separate Petri dish containing growth medium buffered with 2 mM 2(N-morpholino)-ethane sulfonic acid adjusted to pH 6.0. Cells at the desired stage of development were then placed in another dish containing 1% glutaraldehyde in buffered medium and fixed for 20 min. Gold double-replica supports (Balzers High Vacuum Corp ., Santa Ana, Calif.) were coated with a thin layer of yeast paste. Fixed cells were placed on one support and the second support was placed on top. This "sandwich" was plunged into liquid propane near its melting point and stored in liquid nitrogen. Cells were ultrarapidly frozen using a propane-jet device of the type described by Miiller et al (see reference). Samples were prepared as described above, with the following exceptions: cells were frozen directly in growth medium, without prior fixation; the gold supports used had been hollowed out, leaving a metal thickness of 127 micron and the propane-jet device was used. Samples were fractured and replicated using a Balzers double-replica device in a Balzers BA 360 freeze-etch unit. Fracturing was done at -110°C. The yeast paste allowed recovery of large, intact replicas; these were cleaned in commercial bleach and 70% sulfuric acid at 60°C. Replicas were examined in a JEOL EM 100C at 33,000X magnification.

Image reference: PMID: 7364870.
Ribosome binding sites visualized on freeze-fractured membranes of the rough endoplasmic reticulum. Giddings TH Jr, Staehelin LA. J Cell Biol. 1980 Apr;85(1):147-52.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j01z43qk
title: CIL:1315, Mus musculus, fibroblast. In Cell Image Library

description: The intracellular mobility of MeCP2 (a methylated DNA-binding protein) followed in a mouse fibroblast stably expressing GFP-MeCP2 through a time series of images captured by confocal microscopy after bleaching a 2 micrometer circular area of euchromatin (center, right). Fluorescence recovery after photobleaching (FRAP) is rapid, indicating that MeCP2 in euchromatin is highly mobile.
description: Preparation: whole mounted tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: fluorescence emission
Visualization methods: fluorescent proteins derived from Aequorea victoria
Processing history: unprocessed raw data
description: Images were obtained using a Zeiss 510 Meta confocal microscope with excitation at 488 nm and emission between 505 nm and 530 nm. An initial scan of the cell was followed by the bleaching of a 2 um diameter spot of euchromatin, and 60 successive images recorded at 5 s intervals to measure fluorescence recovery due to MeCP2 mobility.
DOI: 10.6075/j0057f23
title: CIL:13138, 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; colchcine pretreatment
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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: In this colchicine-treated cell, used in an attempt to disrupt its microtubules, we found that microtubules already formed are not disrupted in Paramecium. This open cytoproct shows the microfilaments around the retrieved membrane vesicles. The larger vesicles appear to be expanded ER as ribosomes can be seen on their cytosolic face. A long membrane tubule appears to be bound to a microtubular ribbon that may have its origin at the cytopharynx. TEM taken on 1/16/73 by R. Allen with Hitachi HU11A operating at 60kV. Neg. 8,100X. 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:38702) 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/j0gb235g
title: CIL:13131, 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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: The cytoproct is the site of spent vacuole defecation on the surface of Paramecium. When closed the cytoproct forms a long narrow wavy ridge along the posterior suture. At its apex the ridge is about 0.2µm wide and it can be as much as 12µm or more in length. This ridge has the ability to be pulled down against the approaching spent vacuole where the plasma membrane covering the midline of the ridge will meet and fuse with the membrane of the vacuole. The ridge contains unique fibers on both of its lips that mesh with each other as they meet inside the ridge (see Allen and Wolf, J. Cell Sci. 14:611-631, 1974). TEM taken on 4/19/79 by R. Allen with Hitachi HU11A operating at 60kV. Neg. 10,000X. 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:12343) 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/j06w99cb
title: CIL:1757, 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: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: 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 2 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j03x85xw
title: CIL:1750, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 2 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j0h13157
title: CIL:12642, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of early endosomes in which the membranes are easily seen as a tripartite track. Gold, labeling the C6 antigen, is observed only in the body of the early endosome and not in the coated evagination or small coated vesicle lying nearby, which may be a newly released carrier vesicle or a coated evagination still attached to an early endosome. TEM taken on 5/14/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are outlined in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Epson Perfection V750 Pro. This image is best used 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j06d5rqv
title: CIL:12644, Insect host: Dalbulus elimatus (Hemiptera, Cicadellidae), epithelial cell, bacteria. In Cell Image Library

description: Epithelial cells (ec) of the midgut. Spiroplasmas are bacteria in the Class Mollicutes that are frequently associated with insects and/or plants. These electron micrographs show symbiotic/ commensal spiroplasma-like organisms (SLOs) in the midgut/ filter chamber of a leafhopper, Dalbulus elimatus. SLOs found in this insect are long and tubular shaped with a tip structure (t). These SLOs (S) were found in great numbers in the gut lumen (lu) frequently associated with gut microvilli, but unlike the plant-pathogenic mollicutes, they did not seem to invade the gut epithelium (ec) or other tissues in their leafhopper hosts. This image is related to Fig. 1 in Arch. Microbiol (2011) 193:35-44.
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: sectioned tissue
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
Processing history: unprocessed raw data
DOI: 10.6075/j0057f6w
title: CIL:1265, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 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: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
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/j0833r40
title: CIL:12626, Homo sapiens, stem cell. In Cell Image Library

description: Human embryonic stem cell colony. This phase contrast image shows a human embryonic stem cell colony growing on Matrigel, a substrate that supports attachment of hESC. The Matrigel forms a thin coating under the cells and is not directly visible in this image. This is a live cell preparation that was imaged using a Nikon inverted Eclipse microscope.
Notes
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
DOI: 10.6075/j0dn4471
title: CIL:12625, Homo sapiens, Mus musculus, stem cell, fibroblast. 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
description: Human embryonic stem cell colonies. This phase contrast image shows two human embryonic stem cell colonies growing on a feeder layer of mouse embryonic fibroblasts. The stem cells actually grow in between the fibroblasts. The feeder layer helps provide nutrition for the stem cells as well as factors that keep them from differentiating. This is a live cell preparation that was imaged using a Nikon inverted Eclipse microscope.
DOI: 10.6075/j0s75fgj
title: CIL:12624, Mesocricetus auratus, oocyte. In Cell Image Library

description: Surface of the zona pellucida surrounding a hamster oocyte. This scanning electron micrograph shows the zona pellicida around a hamster oocyte at high magnification. The zona pellicida has a complex weave and is comprised of three glycoproteins, ZP1, ZP2 and ZP3. The sample was fixed using glutaraldehyde and osmium tetroxide, dehydrated in ethanol, critically point dried, coated with gold, and examined in a Phillips XL30 FEG scanning electron microscope. Magnification: 5851x.
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; critical_point dried specimen
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
Data qualification: Raw
DOI: 10.6075/j0765czp
title: CIL:28769. In Cell Image Library

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.30 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.15468/dl.nvh6f2
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Hordeum vulgare"
 ]
}

 The dataset includes 60 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009604-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0862f6t
title: CIL:24807, Xenopus laevis, keratocyte. In Cell Image Library

description: Localization of XAC (Xenopus ADF/cofilin) in Xenopus keratocytes done with immuno-EM. A higher mag view of a localized region of the cell is shown in CIL 24808. Image corresponds to Figure 8g from J Cell Biol. 1999 May 31;145(5):1009-26. A fluorescence image showing XAC and phalloidin labelin is available as CIL 24807.
description: Preparation: glutaraldehyde fixed tissue; permeabilized tissue; polyethelyene glycol
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: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
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).
DOI: 10.6075/j0bp02dn
title: CIL: 53071, 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: Image 4, z=17 from SC_028
description: One z layer of a z-stack at the given image
DOI: 10.6075/j09c6wj7
title: CIL:12634, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of two parasomal sacs that are oriented perpendicular to the basal bodies. The top parasomal sac has a clathrin cage around it's coated pit area. The P-face of the plasma membrane has some IMPs, particularly around the neck of the basal body. Alveoli contain some non-etchable material. Striated bands are anchored to the cytosolic face of the inner alveolar membrane to which an inconspicuous epiplasm is bound. Fractured kinetodesmal fibers show evidence of longitudinally ordered packing of subunits even though cross striations are more prominent in thin sections. Additional interpretation is available at Chapter 8, Image 9 at the link below. TEM taken on 6/4/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 24,800X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0v1240z
title: CIL:12629, Homo sapiens, embryonic stem cell. In Cell Image Library

description: Images were deconvolved using Nikon Elements software.
description: Preparation: chemically fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: deconvolution
description: Thick microtubule bundles are organized around the periphery of each stem cell in human embryonic stem cell colonies. Human embryonic fibroblasts were grown on a layer of mouse embryonic fibroblasts which provide nutrients and help maintain pluripotency of the colonies. The sample has been labeled with an antibody to tubulin using standard protocols for immunolabeling.