cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09z951t
title: CIL:40205, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt
Data qualification: Processed
description: Single computed slice through a tomographic reconstruction of the cell body of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. The reconstruction is the 13th in a series of 26 serial reconstructions through the cell soma. All 26 images can be found in this image group within the Cell Library, and the complete reconstruction can be viewed in the Cell centered database, accession # 7503.
description: Detailed methods can be found at the CCDB link provided. Briefly, one month old male mouse (C57BL/6NHsd) was perfused with Ringer's solution for 2 minutes followed by 2% glutaraldehyde and 2% paraformaldehyde in 0.15M sodium cacodylate buffer, pH 7.4. Further dissection of tissue was followed with postfixation using 1% OsO4, additional staining using 2% uranyl acetate, processed for embedding in durcupan ACM resin, and sectioned at a thickness of 5µm thick. Serial tomograms were produced from single tilt images using a JEOL4000, with 8k x 8k CCD camera, 5000X, 400.0 keV).
DOI: 10.6075/j0vx0gnt
title: CIL:40199, Mus musculus, CNS neuron (sensu Vertebrata), astrocyte of the hippocampus. In Cell Image Library

description: Wide field mosaic of mouse hippocampus immunolabeled for the hemichannel pore protein pannexin 1 (shown here in green), the astrocytic intermediate filament GFAP (colorized blue) and the gap junction protein connexin 43 (colorized red). The section was also counterstained with DAPI (not shown). 176 tiles (16x11 frames) were digitally stitched together to generate a 3D mosaic montage. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Mouse brains were perfused with 4% paraformaldehyde, and sections at 50 µm on a vibratome. Tissue was immunostained using the Rabbit Cx43 antibody (Sigma) 1:600; Guinea pig GFAP antibody (discontinued) 1:600; and Chicken Panx1 antibody (4515) 1:250, 72hour incubation at 4C. Secondary antibodies used were donkey-anti-rabbit Al647; donkey-anti-Guinea pig-RRX; and donkey-anti-chicken-FITC, 2.5hours incubation at room temperature. Individual images were gathered using an Olympus Fluoview 1000, with an Olympus PlanApo 60X oil, 1.42 NA.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde 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; Alexa Fluor 647
Data qualification: Processed
DOI: 10.6075/j0b27vdm
title: CIL:40182, Homo sapiens, pyramidal cell, neuron of cerebral cortex. In Cell Image Library

description: Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
description: Single image from a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Ellisman et al. Neuronal fibrillar cytoskeleton and endomembrane system organization in Alzheimers disease, In Alteration of the Neuronal Cytoskeleton in Aging and Dementia, GP Perry (Ed,).pp, 61-73, Plenum Publ, Corp, New York, 1988.
DOI: 10.6075/j0ft8m5g
title: CIL:40179, Chlorocebus pygerythrus, epithelial cell. In Cell Image Library

description: For ultrastructural morphological investigations, SARS-CoV-infected Vero E6 cells were pre-fixed (for biosafety reasons) overnight with 3% paraformaldehyde in 0.1M PHEM buffer (60 mM piperazide-1,4-bis[2-ethanesulfonic acid], 25 mM HEPES, 2 mM MgCl2, 10 mM EGTA) at various time points after infection. For cryo-fixation, cell monolayers adhered to Thermanox coverslips (Nunc, Denmark) were plunged into liquid ethane. Freeze substitution was performed at -90°C in an automated freeze-substitution system (Leica, Austria) using an FS medium consisting of 90% acetone and 10% water, containing 1% osmium tetroxide and 0.5 % uranyl acetate. After washing with pure acetone at RT, the samples were embedded in epoxy LX-12 resin. Thin sections were collected on 100 Mesh grids, 1.25% pioloform support film contrasted with uranyl acetate and lead hydroxide and subsequently viewed at 80 kV with a Philips CM-10 transmission electron microscope (Philips, The Netherlands).
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Visualization methods: uranyl salt
Data qualification: Processed
description: Single computed slice through a dual axis tilt electron tomographic reconstruction of a freeze-substituted VeroE6 cultured cell infected with the SARS-CoV. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Knoops et al. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biol. 2008 6(9):e226. PMID: 18798692
DOI: 10.6075/j0qc03m2
title: CIL:40178, Chlorocebus pygerythrus, epithelial cell. In Cell Image Library

description: For ultrastructural morphological investigations, SARS-CoV-infected Vero E6 cells were pre-fixed (for biosafety reasons) overnight with 3% paraformaldehyde in 0.1M PHEM buffer (60 mM piperazide-1,4-bis[2-ethanesulfonic acid], 25 mM HEPES, 2 mM MgCl2, 10 mM EGTA) at various time points after infection. For cryo-fixation, cell monolayers adhered to Thermanox coverslips (Nunc, Denmark) were plunged into liquid ethane. Freeze substitution was performed at -90°C in an automated freeze-substitution system (Leica, Austria) using an FS medium consisting of 90% acetone and 10% water, containing 1% osmium tetroxide and 0.5 % uranyl acetate. After washing with pure acetone at RT, the samples were embedded in epoxy LX-12 resin. Thin sections were collected on 100 Mesh grids, 1.25% pioloform support film contrasted with uranyl acetate and lead hydroxide and subsequently viewed at 80 kV with a Philips CM-10 transmission electron microscope (Philips, The Netherlands).
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Visualization methods: uranyl salt
Data qualification: Processed
description: Single computed slice through a dual axis tilt electron tomographic reconstruction of double membrane vesicles in a freeze-substituted VeroE6 cultured cell infected with the SARS-CoV. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Knoops et al. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biol. 2008 6(9):e226. PMID: 18798692
DOI: 10.6075/j0bv7grg
title: CIL:40196, Rattus norvegicus, astrocyte of the hippocampus, astrocyte. 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: intracellular filling
Visualization methods: lucifer yellow; Alexa Fluor 568; X-Rhodamine; primary antibody plus labeled secondary antibody
Data qualification: Processed
description: Male Sprague Dawley rats were anesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with either 5% aq. lucifer yellow. The astrocytes were filled using a 0.5 Hz pulses of
current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C, and subsequently immunostained. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000
(Hercules, CA) attached to a Nikon E600FN
(Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60× oil objective (NA 1.4). Optical z resolution is 0.25µm. Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injections of protoplasmic a 1-week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow (green) and immunostained to reveal the localization of glial-specific proteins S-100 (red) and GFAP (blue). Optical sections were generated with a single photon confocal microscope. 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/j0gm87d9
title: CIL:40195, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

description: Detailed methods can be found at the CCDB link provided. Briefly, one month old male mouse (C57BL/6NHsd) was perfused with Ringer's solution for 2 minutes followed by 2% glutaraldehyde and 2% paraformaldehyde in 0.15M sodium cacodylate buffer, pH 7.4. Further dissection of tissue was followed with postfixation using 1% OsO4, additional staining using 2% uranyl acetate, processed for embedding in durcupan ACM resin, and sectioned at a thickness of 5µm thick. Serial tomograms were produced from single tilt images using a JEOL4000, with 8k x 8k CCD camera, 5000X, 400.0 keV).
description: Single computed slice through a tomographic reconstruction of the cell body of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. The reconstruction is the 18th in a series of 26 serial reconstructions through the cell soma. All 26 images can be found in this image group within the Cell Library, and the complete reconstruction can be viewed in the Cell centered database, accession # 7503.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt
Data qualification: Processed
DOI: 10.6075/j00p104h
title: CIL:40191, Homo sapiens, pyramidal cell, neuron of cerebral cortex. In Cell Image Library

description: Single image from a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Ellisman et al. Neuronal fibrillar cytoskeleton and endomembrane system organization in Alzheimers disease, In Alteration of the Neuronal Cytoskeleton in Aging and Dementia, GP Perry (Ed,).pp, 61-73, Plenum Publ, Corp, New York, 1988.
description: Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
DOI: 10.6075/j0jm29rz
title: CIL:40190, Homo sapiens, pyramidal cell, neuron of cerebral cortex. In Cell Image Library

description: Single image from a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Ellisman et al. Neuronal fibrillar cytoskeleton and endomembrane system organization in Alzheimers disease, In Alteration of the Neuronal Cytoskeleton in Aging and Dementia, GP Perry (Ed,).pp, 61-73, Plenum Publ, Corp, New York, 1988.
description: Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
description: Single image from a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Ellisman et al. Neuronal fibrillar cytoskeleton and endomembrane system organization in Alzheimers disease, In Alteration of the Neuronal Cytoskeleton in Aging and Dementia, GP Perry (Ed,).pp, 61-73, Plenum Publ, Corp, New York, 1988.
DOI: 10.6075/j07944tn
title: CIL:40173, 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 Alexa 568. 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 immunostained and 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 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: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Data qualification: Processed
description: Projection through merged optical section series of adjacent hippocampal astrocytes from a 1-week old male rat, injected with Lucifer Yellow (green) and Alexa568 (red) respectively, and immunolabeled for GFAP (blue), imaged with confocal microscopy. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86. 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/j0r78fbk
title: CIL:40168, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

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; Hoechst 33342
Data qualification: Processed
description: Large scale brain mosaic through level of cerebellar vermis of a wild type mouse labeled for alpha synuclein (green) and a nuclear stain (blue). 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: A wildtype adult male mouse (C57BL/6 * DBA/2, 291 days) 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. Hoescht 33342 was used to stain nuclei (30 min). After rinsing in PBS, sections were mounted on slides and coverslipped using Gelvatol. Sections were imaged using a BioRad RTS 2000MP Multiphoton, with a 60X, NA 1.4 objective. Final multi-panel montage is a projection through 5 z planes.
DOI: 10.6075/j0kp81hs
title: CIL:40167, Mus musculus, peripheral neuron, myelinating Schwann cell. In Cell Image Library

description: Tissue was obtained from a postnatal day 3 male mouse and prepared using conventional EM tissue preservation methods. Images were obtained using a JEOL 4000 microscope. A double tilt tomogram spanned -60 to 60° at 2° increments. Magnification: 40000X, accelerating voltage: 400.0 KeV.
description: Single slice through a double tilt tomogram of the paranodal region of the Node of Ranvier from mouse sciatic nerve. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information see: Sosinsky et al. (2005) Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography. Neuroinformatics. 3(2):133-62. PMID: 15988042
description: Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
DOI: 10.6075/j0445ktr
title: CIL:40164, Mus musculus, peripheral neuron, myelinating Schwann cell. In Cell Image Library

description: Single slice through a single tilt tomogram of the Node of Ranvier from mouse sciatic nerve. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information see: Sosinsky et al. (2005) Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography. Neuroinformatics. 3(2):133-62. PMID: 15988042
description: Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: Tissue was obtained from a postnatal day 3 male mouse. Images were obtained using a JEOL 4000 microscope. Single tilt tomogram spanned -60 to 60° at 2° increments. Magnification: 20000X, accelerating voltage: 400.0 KeV.
DOI: 10.6075/j0vt1rv5
title: CIL: 50683, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. In Cell Image Library

description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
1.4_Cell_1_Stack_Filtered is a multipage TIFF file filtered using mean shift (kernel: 3D, 3 &gt; max distance X & Y: 3 &gt; noise spread: 1.0), unsharp (unit: 8 &gt; kernel: 3D, 3 &gt; standard deviation: 1.0 &gt; unsharp factor: 1.0), and histogram balancing (reference slide #170). 
This file is a part of Dataset 1, comprised of files related to the Cell #1 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
description: Imaging mode: Serial electron microscopy; focused ion beam scanning electron mictoscopy (FIB-SEM)
Visualization methods: Heavy metal stain (osmium tetroxide, potassium ferrocyanide, tannic acid), immunogold labeling using 10 nm gold beads