cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0833s5v
title: CIL:40220, 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: 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 3rd 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.
DOI: 10.6075/j0x63n2s
title: CIL:40249, Canis lupus familiaris, epithelial cell. In Cell Image Library

description: MDCK cells stably expressing two internal 4C domains in the C-terminus (FLNCCPGCCME)-tagged Cx43 (Cx43-4C309/337) were labeled for 1 h at 37 degrees C with 180 nM FlAsH-EDT2/12.5 uM EDT in Hanks balanced salt saline (HBSS). Free and non-specifically bound FlAsH was removed by washing with 2,3-dimercapto-1-propanol (BAL, 500 uM, 20min at 37 degrees C in HBSS). Time-lapse imaging was conducted using an Olympus FluoView1000 confocal microscope equipped with a temperature controlled chamber (at 37 degrees C) and a 60X 1.42 NA objective. Medium: Opti-MEM supplemented with 5% FBS covered with a glass coverslip.
description: A single frame from a time-lapse animation of FlAsH-labeled MDCK cells expressing Cx43-4C309/337 (green) showing their rearrangement and fate during and after mitosis. In the time-lapse series, which can be accessed using the link provided to the Cell Centered Database, FlAsH fluorescence excitation z series along with a transmitted DIC image were recorded every 6 min for a total duration of about 5 h. 3D volume reconstructions from confocal image stacks over time are displayed at a rate of two frames per minute. From Supplemental movie 2 from Boassa et al. (2010) Traffic. PMID 20716111.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: living tissue; dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Data qualification: Processed
DOI: 10.6075/j0dv1k06
title: CIL:40212, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

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 22nd 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).
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/j0vm4cdv
title: CIL:40028, 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 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.
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: 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.
DOI: 10.6075/j0s182mv
title: CIL:40030, 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: 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.
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
DOI: 10.6075/j0wm1dj7
title: CIL:40018, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Visualization methods: intracellular filling
Data qualification: Processed
description: Summed Z projection through a through-focus series of a medium spiny neuron from the neostriatum of a dopamine-transporter knock out mouse, filled with Lucifer Yellow and then photooxidized. The neuron is not completely contained within the section so part of it is missing. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database, where the reconstruction of the entire cell can also be found.
description: Tissue was prepared from a 6 month adult male mouse strain, C57BL/129SvJ with a dopamine transporter knock-ou. Tissue sections, 100µm, were generated using a vibratome. The entire through series of images were gathered using a Bio-Rad 1024 confocal with a Zeiss Plan Apochromat 63X 1.4 NA.
DOI: 10.6075/j0cr5tgj
title: CIL:40029, 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/j0rv0nvz
title: CIL:40020, Rattus norvegicus, Purkinje cell. 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
Visualization methods: uranyl salt
Data qualification: Processed
description: 1. Fixation: A 21 day old rat was perfused with a solution of 2% of paraformaldehyde/2.5% of glutaraldehyde in 0.15 M cacodylate buffer according to the protocol described in (Giepmans, 2005 see original publication for details). Brain was taken out and post-fixed in same fixative for 2 hrs at 4¿C. For brain tissue, 100mm thick sections were kept in the fixative solution until HPF. 

2. High Pressure Freezing: Brain sections were cut with 1.8 mm tissue puncher. This step ensures that the proper size of brain tissue will fit into the shallow side of a 100 mm-deep well in the type A HPF brass planchette. For peripheral nerve tissue, the nerves were carefully trimmed to a proper length in order to fit into the type A freezing hats. Trimmed brain or nerve tissue was loaded into the planchettes and the well was filled with 1-hexadecene. The planchette was then covered with the flat side of brass type B planchette, quickly loaded into a freezing holder and frozen with the Bal-Tec HPM 010. 
 
Freeze-substitution procedure: After freezing, the planchette sandwiches were separated under liquid nitrogen and the specimen/type A hats were placed into cryo-vials and stored under liquid nitrogen or subsequently placed into the freeze substitution device. The first substitution media was a solution of filled with freshly made 0.1% tannic acid (EM grade, from Polysciences Inc., Warrington, Pennsylvania) in acetone (EM grade from Fullam Inc., Latham, New York). After 24 hours, samples were then washed three times in cold acetone over a 2 hour period. The solution was changed to 2% osmium tetroxide in acetone for 48 hrs. The temperature was slowly raised to 20 deg C. The specimens were rinsed three times at room temperature for 10 minutes in acetone. Tissues were removed from the planchettes after the last wash step. The total time for this procedure is 113 hrs.

Infiltration and embedding: Infiltration was conducted over 3 days followed by embedding in Durcupan ACM resin (Electron Microscopy Science Inc., Hatfield, PA). Samples were infiltrated in 30% Durcupan in acetone for 4 hours and 50% Durcupan overnight. The next day, the specimens were placed into 70% Durcupan for 4 hours, 90% over 2 hours and were placed in 100% Durcupan for overnight incubation. After two incubations in fresh 100% Durcupan, the sample was then polymerized at 60deg C for 2 days.
description: Single computed slice through a tomographic reconstruction of a spine synapse from the molecular layer of the cerebellar cortex from tissue that was prepared from a combination of chemical fixation and high pressure freezing. The contrast was adjusted and the image downsampled to 8 bits from the submitted data for display purposes.
DOI: 10.6075/j0h995b5
title: CIL:40022, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Z projection through a through-focus series of a medium spiny neuron of the neostriatum from a dopamine transporter knock out mouse, injected with Lucifer Yellow and then photoconverted. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database, where the reconstruction of the entire cell can also be found.
description: Preparation: formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Visualization methods: intracellular filling; lucifer yellow
Data qualification: Processed
description: Tissue was prepared from a 6 month adult male mouse strain, C57BL/129SvJ. Tissue sections, 100µm, were generated using a vibratome. The entire through series of images were gathered using a Bio-Rad Radiance 2000 with a 40X 0.75 NA.
DOI: 10.6075/j0dj5frt
title: CIL:40015, Rattus norvegicus. In Cell Image Library

description: 1. Fixation: A 21 day old rat was perfused with a solution of 2% of paraformaldehyde/2.5% of glutaraldehyde in 0.15 M cacodylate buffer according to the protocol described in (Giepmans, 2005 see original publication for details). Brain was taken out and post-fixed in same fixative for 2 hrs at 4°C. For brain tissue, 100mm thick sections were kept in the fixative solution until HPF. 

2. High Pressure Freezing: Brain sections were cut with 1.8 mm tissue puncher. This step ensures that the proper size of brain tissue will fit into the shallow side of a 100 mm-deep well in the type A HPF brass planchette. For peripheral nerve tissue, the nerves were carefully trimmed to a proper length in order to fit into the type A freezing hats. Trimmed brain or nerve tissue was loaded into the planchettes and the well was filled with 1-hexadecene. The planchette was then covered with the flat side of brass type B planchette, quickly loaded into a freezing holder and frozen with the Bal-Tec HPM 010. 
 
Freeze-substitution procedure: After freezing, the planchette sandwiches were separated under liquid nitrogen and the specimen/type A hats were placed into cryo-vials and stored under liquid nitrogen or subsequently placed into the freeze substitution device. The first substitution media was a solution of filled with freshly made 0.1% tannic acid (EM grade, from Polysciences Inc., Warrington, Pennsylvania) in acetone (EM grade from Fullam Inc., Latham, New York). After 24 hours, samples were then washed three times in cold acetone over a 2 hour period. The solution was changed to 2% osmium tetroxide in acetone for 48 hrs. The temperature was slowly raised to 20 deg C. The specimens were rinsed three times at room temperature for 10 minutes in acetone. Tissues were removed from the planchettes after the last wash step. The total time for this procedure is 113 hrs.

Infiltration and embedding: Infiltration was conducted over 3 days followed by embedding in Durcupan ACM resin (Electron Microscopy Science Inc., Hatfield, PA). Samples were infiltrated in 30% Durcupan in acetone for 4 hours and 50% Durcupan overnight. The next day, the specimens were placed into 70% Durcupan for 4 hours, 90% over 2 hours and were placed in 100% Durcupan for overnight incubation. After two incubations in fresh 100% Durcupan, the sample was then polymerized at 60deg C for 2 days.
description: Single computed slice through a tomographic reconstruction of neuropil from the molecular layer of the cerebellar cortex from tissue that was prepared from a combination of chemical fixation and high pressure freezing. The contrast was adjusted and the image downsampled to 8 bits from the submitted data for display purposes.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed