cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0nz874q
title: CIL: 52314, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
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: Tile x=4, y=2, z=16 from BL_024216_Myc_Terc
DOI: 10.6075/j0np24jt
title: CIL:40254, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt
Data qualification: Processed
description: Single slice through a serial section reconstruction of the optic nerve head in the area of transition between myelinated and unmyelinated axons the mouse obtained through serial section scanning 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. For more information, see: Nguyen et al. Myelination transition zone astrocytes are constitutively phagocytic and have synuclein dependent reactivity in glaucoma. Proc Natl Acad Sci U S A. 2011. PMID:21199938
description: The animal was perfused with Ringer's followed by 2% PFA / 2.5% glutaraldehyde. The tissue was postfixed in the same fixative for 2 hours on ice. The eye was enucleated and the optic nerve head was dissected for sagittal longitudinal section.

The tissue was placed into solution containing 3% potassium dichromate and 2% osmium tetroxide in ddH2O. The samples were allowed to sit at room temp for 3 hours.
 
The tissue washed with ddH2O at room temp 3x 5 minutes and placed in filtered thiocarbohydrazide(TCH) solution(0.1 g TCH in 10 mL ddH2O) for 30 minutes at room temp.

After washes with ddH2O at room temp (3x 5 minutes) tissue was placed in 2% osmium in ddH20 for an hour at room temp.

Another series of washes (3x 5 minutes) was followed with 1% aqueous uranyl acetate overnight in fridge.

The next day, 0.066g of lead nitrate was dissolved in 10 mL aspartic acid solution and adjust pH to 5.5 with 1N KOH and incubated at 60° C for 30 minutes taking care that no precipitate formed.

Tissue was removed from 1% UA, washed (ddH2O, 3x 5 minutes) and placed in the lead aspartate solution, 60°C, 30 minutes. 
After washes, tissue was dehydrated and embedded in Durcupan according to standard protocol.

This image was acquired at 1400X using a Gatan 3View system on FEI Quanta microscope, and is a mosaic of 2 x 3 (x,y) tiles.
DOI: 10.6075/j0jw8f17
title: CIL:40245, Felis catus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: Single computed slice from a tomographic reconstruction through the Calyx of Held of an adult cat. The mitochondrion in the presynaptic terminal exhibits a structural specialization termed the mitochondrial adherens complex. 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: Perkins et al. (2101) The micro-architecture of mitochondria at active zones: electron tomography reveals novel anchoring scaffolds and cristae structured for high-rate metabolism. J Neurosci. PMID: 20089910
DOI: 10.6075/j0f47p8c
title: CIL:40243, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

description: Single computed slice through a serial tomogram consisting of 26 single tilt tomographic reconstructions of the soma of an astrocyte in stratum radiatum of hippocampal area CA1 of an adult mouse. 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: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Visualization methods: uranyl salt
Data qualification: Processed
description: One month old C57 male black mouse 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, at 35 degrees Celsius for 10 minutes. Tissue was removed and fixed on ice for 1-2 hours. During this time the tissue was further dissected.

Dissection was followed with washes (5x5 minutes in cold 0.15M sodium cacodylate buffer), and postfixation (1% OsO4 in 0.15M sodium cacodylate buffer on ice for 1 hour), another series of rinses in cold ddH2O 4x5 minutes then 2% uranyl acetate in ddH2O on ice for 2 hours. After staining, tissue was rinsed, dehydrated and embedded in durcupan ACM resin using standard embedding procedures.
DOI: 10.6075/j0pn95s0
title: CIL:40241, Rattus norvegicus, CNS neuron (sensu Vertebrata), hippocampal neuron. In Cell Image Library

description: Rat brain was perfused with 4% paraformaldehyde and sectionedrain section was immunolabeled for PMCA1a using CR1a antibody from Emanuel Strehler (1:2000). Secondary antibody was conjugated to Alexa Fluor 568. Section was then counterstained with Hoescht 33342 (Invitrogen) to visualized all cell nuclei. The sections were coverslipped in Gelvatol. Images were acquired using a BioRad RTS2000 with a Nikon 60X N.A. 1.4 oil-immersion objective. 46 x 19 maximum projection images were tiled together to generate this composite image.
description: Preparation: formaldehyde 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; differences in adsorption or binding of stain
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 568; Hoechst 33342
Data qualification: Processed
description: Large scale mosaic of a parasagittal section of rat brain stained with an antibody against a plasma membrane calcium-dependent ATPase, PMCA1a (shown here in red), and counter stained with Hoescht 33342 to reveal cell nuclei (shown here in green). 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: Kenyon et al.(2010) J Comp Neurol. 518(16):3169-83, PMID 20575074.
DOI: 10.6075/j07m0821
title: CIL:40261, Mus musculus, astrocyte of the cerebellum, CNS neuron (sensu Vertebrata). In Cell Image Library

description: The mouse was anesthetized with Nembutal and then perfused with Ringer's containing heparin and xylocaine and bubbled with 95% O2 / 5% CO2. The mouse was then perfused with 2.5% glutaraldehyde / 2% PFA in cacodylate buffer containing 2 mM CaCl.

The brain was removed and placed in same post-fix for 2 hours and 15 minutes in fridge.

The brain was cut in to 100 um thick vibratome sections in ice cold cac buffer with 2mM Ca.

The slices were washed in cac w/ Ca for 30 minutes in fridge.

The slices were placed into 2% OsO4 / 1.5% potassium ferrocyanide in cac w/ Ca at room temp for 1 hour.

The slices were washed 3x 2 minutes with ddH2O and then placed into 1% aq. thiocarbohydrazide for 20 minutes at room temp.

The slices were washed 2x 2 minutes with ddH2O and then placed in 2% aq. OsO4 for 30 min at room temp.

The slices were washed 3x 2 min with ddH2O and then placed in 2% aq. UA overnight in fridge.

The next day the slices were washed 3x 10 min in ddH2O and then placed in lead aspartate solution in 60 degree oven for 30 min.

The slices were washed 3x 5min in ddH2O at room temp.

The slices were dehydrated in series of ice cold EtOH solutions (70%, 90%, 100%, 100%; 10 min each).

The slices were placed in ice-cold acetone for 10 min and left at room temp

The slices were placed in room temp acetone for 10 minutes.

The slices were placed in 25% Durcupan for 3 hours. The slices were placed in 50% Durcupan overnight.

The slices were placed in 75% Durcupan for 3 hours. The slices were placed in 100% Durcupan overnight.

The slices were flat-embedded in fresh 100% Durcupan and left in 50 degree oven for 48 hours.

Images gathered on an FEI Quanta 200 FEG SEM with Gatan 3 View microscope, magnification, 2500.0 X, accelerating voltage, 2.5 kV.
description: Single slice of a processed serial block face SEM imaging data set through the molecular layer of the cerebellum of an adult mouse. Data have been converted from 16 bit to 8 bit and low pass filtered for smoothing. 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: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: back-scattered_electron imaging
Data qualification: Processed
DOI: 10.6075/j0mw2h8j
title: CIL:40259, Mus musculus, astrocyte of the cerebellum, CNS neuron (sensu Vertebrata). In Cell Image Library

description: The mouse was anesthetized with Nembutal and then perfused with Ringer's containing heparin and xylocaine and bubbled with 95% O2 / 5% CO2. The mouse was then perfused with 2.5% glutaraldehyde / 2% PFA in cacodylate buffer containing 2 mM CaCl.

The brain was removed and placed in same post-fix for 2 hours and 15 minutes in fridge.

The brain was cut in to 100 um thick vibratome sections in ice cold cac buffer with 2mM Ca.

The slices were washed in cac w/ Ca for 30 minutes in fridge.

The slices were placed into 2% OsO4 / 1.5% potassium ferrocyanide in cac w/ Ca at room temp for 1 hour.

The slices were washed 3x 2 minutes with ddH2O and then placed into 1% aq. thiocarbohydrazide for 20 minutes at room temp.

The slices were washed 2x 2 minutes with ddH2O and then placed in 2% aq. OsO4 for 30 min at room temp.

The slices were washed 3x 2 min with ddH2O and then placed in 2% aq. UA overnight in fridge.

The next day the slices were washed 3x 10 min in ddH2O and then placed in lead aspartate solution in 60 degree oven for 30 min.

The slices were washed 3x 5min in ddH2O at room temp.

The slices were dehydrated in series of ice cold EtOH solutions (70%, 90%, 100%, 100%; 10 min each).

The slices were placed in ice-cold acetone for 10 min and left at room temp

The slices were placed in room temp acetone for 10 minutes.

The slices were placed in 25% Durcupan for 3 hours. The slices were placed in 50% Durcupan overnight.

The slices were placed in 75% Durcupan for 3 hours. The slices were placed in 100% Durcupan overnight.

The slices were flat-embedded in fresh 100% Durcupan and left in 50 degree oven for 48 hours.

Images gathered with a Gatan 3View system on FEI Quanta microscope, magnification, 5000.0 X, accelerating voltage, 2.0 kV.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: back-scattered_electron imaging
Data qualification: Processed
description: Single slice from a cropped and contrast-adjusted serial section reconstruction from the molecular layer of the cerebellar vermis of the adult mouse generated from serial block face SEM. 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/j0736q69
title: CIL:40273, Anethum graveolens, pollen. In Cell Image Library

description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
description: Scanning electron micrograph of Anethum graveolens (Dill) 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: 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
DOI: 10.6075/j0sf2w9m
title: CIL:40253, 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/j0vd6zkt
title: CIL:40082, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

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 NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM 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.
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: 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 then ready to be immunolabeled. The rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. 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.
DOI: 10.6075/j0pv6kgv
title: CIL:40094, 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 then ready to be immunolabeled. The rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. 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: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
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 NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM 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/j0tm7b71
title: CIL:40093, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. 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; 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 a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM 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.
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 then ready to be immunolabeled. The rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. 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.