cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0736r1g
title: CIL:39992, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; tissue in epoxy resin embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Visualization methods: intracellular filling; lucifer yellow
Data qualification: Processed
description: A single computed slice from a tomographic reconstruction of a lucifer yellow injected spiny dendrite from a striatal medium spiny neuron from the neostriatum of a dopamine transporter knock out mouse. This reconstructed image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database.
description: Tissue from mouse strain: B6;129-/Slc6a3 tm2Mca, dopamine transporter knockout. Individual cells in fixed tissue were injected with Lucifer yellow and stored in 4% paraformaldehyde at 4° C. Fluorescence was photoconverted using DAB and a confocal laser light source. After this process, tissue was washed thoroughly in PBS and processed for EM by osmication, dehydration, and embedding in epoxy resin. For detailed methods, see the protocol provided in the CCDB. The tomogram was generated using an Hitachi UHVEM. Single tilt images spanned -70 to 70° in 2° increments. Magnification, 3000X, accelerating voltage, 3.0 MeV.
DOI: 10.6075/j01836m6
title: CIL:40017, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; tissue in epoxy resin embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Visualization methods: intracellular filling
Data qualification: Processed
description: Representative electron micrograph from a tomographic reconstruction of a selectively stained spiny dendrite from a striatal medium spiny neuron from the neostriatum of a dopamine transporter knockout mouse. This reconstructed image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database.
description: Tissue from mouse strain: B6;129-/Slc6a3 tm2Mca. Individual cells in fixed tissue were injected with Lucifer yellow and stored in 4% paraformaldehyde at 4° C. Fluorescence was photoconverted using DAB and a confocal laser light source. After this process, tissue was washed thoroughly in PBS and processed for EM by osmication, dehydration, and embedding 
in epoxy resin. For detailed methods, see the protocol provided in the CCDB. The tomogram was generated using an Hitachi UHVEM. Single tilt images spanned -66 to 66° in 2° increments.
DOI: 10.6075/j0st7pzb
title: CIL:40010, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with either 5% aqueous LY in 200 mM KCl. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were then ready to be immunolabeled. The rabbit anti-EphA4 antibody was provided by Dr. Elena Pasquale (The Burnham Institute, La Jolla, CA). EphA4 was subsequently detected using goat anti-rabbit Cy5. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
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: intracellular filling; distribution of epitope
Visualization methods: lucifer yellow; primary antibody plus labeled secondary antibody; Cy5
Data qualification: Processed
description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
DOI: 10.6075/j0k937pt
title: CIL:40006, Mus musculus, regular cardiac myocyte. In Cell Image Library

description: Portion of a single computed slice through a tomographic reconstruction of the myocardium of the left ventricle of a normal mouse. For more information see: Hayashi, T., Martone, M. E., Yu, Z., Thor, A., Doi, M., Holst, M., Ellisman, M. H. and Hoshijima, M., Three-dimensional electron microscopy reveals new details of membrane systems for calcium signaling in the heart. J. Cell Science (2009) PMID: 19295127. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Visualization methods: uranyl salt
Data qualification: Processed
description: Tissue was fixed with 2% paraformaldehyde and 2% glutaraldehyde in 0.15M sodium cacodylate, blocked into small pieces, post-fixed for 1-3 hours, washed 3x10min in 0.15M sodium cacodylate, then incubated in: 0.8% potassium ferrocyanide and 2% osmium tetroxide in 0.15M sodium cacodylate overnight at room temperature. Following another set of washes 2 hours-overnight in 0.15M sodium cacodylate tissue was stained en bloc with 1% uranyl acetate 30min, followed by a brief wash in DDH2O and standard dehydration and embedding. Images were gathered using a JEOL 4000, magnification not given, accelerating voltage, 400.0 kV.
DOI: 10.6075/j0q240c3
title: CIL:40004, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Wild type adult male mouse was anesthetized with nembutal, and perfused with 4% paraformaldehyde + 0.1% glutaraldehyde, followed by 1 hr. postfixation in 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm. Following rinses in phosphate buffer (PBS), sections were blocked (PBS with 3% NGS;1% fish gel, 0.1% Triton X-1000; 1% BSA) for 1 hour, followed by rinses in working buffer (1:10 blocking buffer: PBS). Primary antibody was diluted in working buffer (anti-alpha-SYN; Host = Rabbit used at 1:500), and tissue was covered with aluminum foil and incubated on a shaker in cold room overnight. Tissue was washed with working buffer and incubated in secondary antibody (goat anti-rabbit AlexaFluor 568, 1:50) covered with foil, on cold room shaker, 48 hrs. After rinses, 1:100 Hoescht 33342 was used to stain nuclei (30 min). After rinsing in PBS, sections were mounted on slides and coverslipped using Vectashield. Sections were imaged using a BioRad RTS 2000MP Multiphoton, with a Nikon Plan Fluor 60X, NA 1.4 objective.
description: Large scale brain mosaic at the level of the anterior hippocampus showing the localization of alpha synuclein (green) in a normal mouse. Section was counterstained with a nuclear stain (blue) to reveal the locations of cell somata. This mosaic 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 regarding this project, see: Price DL, Chow SK, MacLean NAB, Hakozaki H, Peltier S, Martone ME, Ellisman MH (2006) High-Resolution Large-Scale Mosaic Imaging using Multiphoton Microscopy to Characterize Transgenic Mouse Models of Human Neurological Disorders. Neuroinformatics. 2006;4(1):65-80.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 568
Data qualification: Processed
DOI: 10.6075/j0qf8t0d
title: CIL:39684, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
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: 10-hour timelapse of the double mutant Clb2dbŒî, Clb5Œî, which has the destruction box region of the CLB2 gene, on the cell cycle control system in budding yeast. The yeast, Saccharomyces cerevisia, are growing in 2% raffinose, since this mutation is inviable in glucose. The images from two experiments done with Wild-type Saccharomyces cerevisiae as a control are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0q23zjj
title: CIL:39721, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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
Data qualification: Raw;spatialmeasurements
description: A nascent digestive vacuole with several acidosome-like vesicles docked at its cytosolic surface. The presence of the microtubules from the oral ribs signifies that this vacuole is still attached to the oral region. These ribbons continue on into the cell as the deep fiber. TEM taken on 1/29/65 by R. Allen with RCA EMU3F operating at 50kV. Neg. 16,000X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0jd4vk1
title: CIL:39741. In Cell Image Library

description: Images of negatively stained chromatin fibers prepared from tandem arrays of a nucleosome positioning sequence reconstituted with purified histones. These samples contained 80 repeats of a 167 bp DNA sequence reconstituted with core histones alone (leftmost image) plus different amounts of linker histone H5 (33%, 67%, and 100% respectively).
 See: Fig 3b in Routh et al. (2008) Nucleosome repeat length and linker histonen stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105:8872-8877.
description: Reconstituted chromatin was fixed with 0.1% glutaraldehyde for 30 min, deposited on glow discharged carbon films, negatively stained with aqueous uranyl acetate, and examined with a Philips 2085 TEM operated at 80 KV.
See also: Routh et al. (2008) Nucleosome repeat length and linker histonen stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 105:8872-8877.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: negative staining; uranyl salt
Processing history: montage
Data qualification: Processed
DOI: 10.6075/j0qv3kth
title: CIL:39720, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The nascent digestive vacuole forms as the membrane of flattened vesicles fuse with the single membrane of the cytopharynx between the lamellae (2 microtubules forming a lamella) that are connected along their length to the membrane at the cytopharynx. Another portion of the forming vacuole is associated with the ends of the 4 element- (4 mt) and 2 element- (2 mt) microtubular ribbons that come from the oral ribs. These ribbons are covered with specialized cytoplasm and do not take part in moving discoidal vesicles to the vesicle fusion region. One feature of the nascent vacuole in Tetrahymena that has not been observed in Paramecium is the presence of coated pits extending from the vacuole membrane. Finally, vesicles previously called lysosomes, which to me resemble the late endosomes, acidosomes, of Paramecium, dock at the growing vacuole. For a review of the literature of phagocytosis in Tetrahymena see Nilsson, Biochemistry and Physiology of Protozoa, 2nd ed., Academic Press, pp. 339-379, 1979; Sattler and Staehelin, J. Ultrastructure Res. 66:132-150, 1979; and Baumert et al., Eur. J. Protistol. 34:291-300, 1998. TEM taken on 8/15/67 by R. Allen with Philips 200 operating at 60kV. Neg 19,200X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0vh5n78
title: CIL:39719, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: The accessory microtubules at the proximal ends of the polykinetids, both in cross section and tangential section, are highlighted at higher magnification. This section shows one parasomal sac as well as several early endosomes under and to the side of the membranelle. TEM taken on 8/25/67 by R. Allen with Philips 200 operating at 60kV. Neg. 28,000X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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
Data qualification: Raw;spatialmeasurements
DOI: 10.34740/kaggle/dsv/13563354
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.6075/j0h130sw
title: CIL:39692, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Transmission electron micrograph of an unbudded yeast cell containing four electron-dense (black) vacuoles. As exemplified here, vacuoles may be either spherical or non-spherical (e.g., lobed). The image contributor asks Library users to answer the following question in the comments box: What are the electron-lucent (white) ~250nm spherical structures?
description: BY4716 is an auxotrophic haploid laboratory strain of the budding yeast Saccharomyces cerevisiae. Its genotype is lys2Δ, mating type alpha and it is derived from S288c. Sections were embedded in LR white resin, mounted on carbon-coated nickel grids and imaged with LEO 912AB at 80kV and 6,300X. All cells in this batch were grown in liquid rich media (YPD pH6.5) at 30˚C with aerated shaking, and cultures were sampled in mid-logarithmic phase. This image is part of a group of untreated cells and cells exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic 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: osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.15468/dl.mpdcaq
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Arundinella hirta"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009254-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0wd40p4
title: CIL:39685, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of the double mutant Clb2dbŒî, Clb5Œî, which has the destruction box region of the CLB2 gene, on the cell cycle control system in budding yeast. The yeast, Saccharomyces cerevisia, are growing in 2% raffinose, since this mutation is inviable in glucose. The images from two experiments done with Wild-type Saccharomyces cerevisiae as a control are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
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: 10.15468/dl.fmwswu
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "BasisOfRecord is one of (Specimen)",
 "InstitutionCode is one of (CM, FHSM, CAS, MCZ, UMMZ, TNHC, NCSM, ASU, APSU, ASNHC, MVZ)",
 "TaxonKey is one of (Anaxyrus hemiophrys [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 183 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009255-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0q52nh1
title: CIL:39690, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Transmission electron micrograph of a budding yeast cell. Electron-dense (black) vacuoles that contain membrane-bound inclusions are visible. The image contributor asks Library users to post comments answering the following questions: What is the tubular organelle protruding into the bud? What about the structure that appears to be an autophagosome encapsulating organellar membrane material located center-right?
description: BY4716 is an auxotrophic haploid laboratory strain of the budding yeast Saccharomyces cerevisiae. Its genotype is lys2Δ, mating type alpha and it is derived from S288c. Sections were embedded in LR white resin, mounted on carbon-coated nickel grids and imaged with LEO 912AB at 80kV and 6,300X. All cells in this batch were grown in liquid rich media (YPD pH6.5) at 30˚C with aerated shaking, and cultures were sampled in mid-logarithmic phase. This image is part of a group of untreated cells and cells exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic 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: osmium tetroxide
Processing history: unprocessed raw data