cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0hx1cqr
title: CIL:6195, Rattus, multipolar neuron. In Cell Image Library

description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0rj4jj3
title: CIL:6191, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
DOI: 10.6075/j0td9xd0
title: CIL:6207, Rattus, multipolar neuron. In Cell Image Library

description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0959hn3
title: CIL:6203, Rattus, multipolar neuron. In Cell Image Library

description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0zk5gpn
title: CIL:6199, Rattus, multipolar neuron. In Cell Image Library

description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
DOI: 10.6075/j03j3c2g
title: CIL:6259, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6271.
DOI: 10.6075/j03777r6
title: CIL:6257, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6265.
DOI: 10.6075/j0s75fbr
title: CIL:6230, Danio rerio, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; heat fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; lead salt; copper salt
Processing history: unprocessed raw data
description: This study on the zebrafish optic tectum is a series of four images with magnifications ranging from the SEM block face overview to of the zebrafish head to high magnification (80,000X) showing optic tectum synapse.
The first image is a bloc face SEM image at 200x of the epon embedded zebrafish head. The second image is another block face SEM low magnification image of the tectum. The third image is a 60,000X TEM image of a OTO fixation and copper lead en bloc staining of zebrafish optic tectum synapse. This image, the fourth image in the series, is a 80,000X TEM image of a zebrafish optic tectum synapse.

Zebrafish 10 dpf Optic Tectum Synapses. Image collected on a JOEL 1230 at 80 kV using a Gatan 967 slow-scan, cooled CCD camera at 80,000X. 70 nm thick section. 

Microwave processing, osmium tetroxoxide/osmid procedure for enhancing membranes, and copper lead en bloc staining.
Procedure for specimen preparation available at http://www.stanford.edu/~redhair/JoAnn_Buchanan.
DOI: 10.15468/dl.2c2h85
title: Occurrence Download

description: A dataset containing 623 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((101.90366 12.03292,133.0195 14.68109,154.96137 50.33662,101.24163 47.31015,91.68936 38.41991,101.90366 12.03292))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lysimachia candida"
 ]
}

 The dataset includes 623 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009684-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0mk6bwz
title: CIL:6229, Danio rerio. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; heat fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: tissue in epoxy resin embedment
Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; lead salt; copper salt
Processing history: unprocessed raw data
description: This study on the zebrafish optic tectum is a series of four images with magnifications ranging from the SEM block face overview to of the zebrafish head to high magnification (80,000X) showing optic tectum synapse.
The first image is a bloc face SEM image at 200x of the epon embedded zebrafish head. This image, the second image in the series, is another block face SEM low magnification image of the tectum. The third image is a 60,000X TEM image of a OTO fixation and copper lead en bloc staining of zebrafish optic tectum synapse. The fourth image is a 80,000X TEM image of a zebrafish optic tectum synapse.

This low magnification image larval zebrafish image of the optic tectum was collected on a Gatan 3View® serial block face scanning electron microscope (SBFSEM). The 3View® is attached to a FEI Quanta 600 FEG SEM. Block face imaging is a way to look at epon embedded specimens using backscattered electrons in the SEM. A diamond knife in the vacuum chamber of the SEM cuts hundreds of ultrathin serial sections, thus gathering a perfected registered stack of images.

Reference for SBFSEM: Denk, W. and H. Horstmann. Serial block face scanning electron microscopy to reconstruct three- dimensional tissue nanostructure. PloS Biology vol 2, 11; e329 doi:10.1371/journal.pbio.0020329

Microwave processing, osmium tetroxoxide/osmid procedure for enhancing membranes, and copper lead en bloc staining.
Procedure for specimen preparation available at http://www.stanford.edu/~redhair/JoAnn_Buchanan.
DOI: 10.6075/j03n22fb
title: CIL:6228, Danio rerio. In Cell Image Library

description: This study on the zebrafish optic tectum is a series of four images with magnifications ranging from the SEM block face overview to of the zebrafish head to high magnification (80,000X) showing optic tectum synapse.
This first image is a bloc face SEM image at 200x of the epon embedded zebrafish head. The second image is another block face SEM low magnification image of the tectum. The third image is a 60,000X TEM image of a OTO fixation and copper lead en bloc staining of zebrafish optic tectum synapse. The fourth image is a 80,000X TEM image of a zebrafish optic tectum synapse.

This image larval zebrafish image was collected on a Gatan 3View® serial block face scanning electron microscope (SBFSEM). The 3View® is attached to a FEI Quanta 600 FEG SEM. Block face imaging is a way to look at epon embedded specimens using backscattered electrons in the SEM. A diamond knife in the vacuum chamber of the SEM cuts hundreds of ultrathin serial sections, thus gathering a perfected registered stack of images.

Reference for SBFSEM: Denk, W. and H. Horstmann. Serial block face scanning electron microscopy to reconstruct three- dimensional tissue nanostructure. PloS Biology vol 2, 11; e329 doi:10.1371/journal.pbio.0020329

Microwave processing, osmium tetroxoxide/osmid procedure for enhancing membranes, and copper lead en bloc staining.
Procedure for specimen preparation available at http://www.stanford.edu/~redhair/JoAnn_Buchanan.
description: Preparation: glutaraldehyde fixed tissue; heat fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: tissue in epoxy resin embedment
Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; lead salt; copper salt
Processing history: unprocessed raw data
DOI: 10.6075/j0gh9h0k
title: CIL:6227, Danio rerio, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This study on the zebrafish optic tectum is a series of four images with magnifications ranging from the SEM block face overview to of the zebrafish head to high magnification (80,000X) showing optic tectum synapse.
The first image is a bloc face SEM image at 200x of the epon embedded zebrafish head. The second image is another block face SEM low magnification image of the tectum. This image, the third image in the series, is a 60,000X TEM image of a OTO fixation and copper lead en bloc staining of zebrafish optic tectum synapse. The fourth image is a 80,000X TEM image of a zebrafish optic tectum synapse.

Larval Zebrafish 10 dpf Optic tectum Synapses
Osmid (osmium imidazole) OTO fixation and copper lead en bloc staining of zebrafish optic tectum. Image collected on a JOEL 1230 at 80 kV using a Gatan 967 slow-scan, cooled CCD camera at 60,000X. 70 nm thick section. 

Microwave processing, osmium tetroxoxide/osmid procedure for enhancing membranes, and copper lead en bloc staining.
Procedure for specimen preparation available at http://www.stanford.edu/~redhair/JoAnn_Buchanan.
description: Preparation: glutaraldehyde fixed tissue; heat fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-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; lead salt; copper salt
Processing history: unprocessed raw data
DOI: 10.6075/j09w0dgf
title: CIL:6269, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 80,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6268.
DOI: 10.6075/j0td9wdk
title: CIL:6265, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6257.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0736pzr
title: CIL:6267, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6258.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data