cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j01v5f30
title: CIL:40248, Canis lupus familiaris, epithelial cell. In Cell Image Library

description: Maximum intensity projection of a confocal z series of MDCK cells expressing Cx43-GFP-4C imaged with confocal microscopy. This image has been downsampled from the raw data image, and time lapse series, both of which can be accessed using the link provided to the Cell Centered Database. For more information, see: Boassa et al. (2010) Trafficking and Recycling of the Connexin43 Gap Junction Protein during Mitosis. Traffic. PMID: 20716111.
description: Madin-Darby canine kidney (MDCK) cells were maintained at 37° C, and 10% CO2 in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum (FBS) (Gibco-BRL, Invitrogen). Transductions were carried out using a retroviral system according to the protocols from the Nolan laboratory (www.stanford.edu/group/nolan). Experiments were conducted on endogenous expressing or stably Cx43-expressing cell lines generated by transduction followed by selection with the antibiotic hygromycin (Gibco-BRL, Invitrogen). In order to image several cells progressing through mitosis, cells were synchronized using a combination of serum starvation and application of aphidicolin (APD), an inhibitor of DNA synthesis, to create an enriched population of cells undergoing mitosis. Confluent cells were trypsinized and grown for about 20 h in the presence of minimal serum and APD, resulting in a G1/S block. The drug was then washed out, normal serum was restored and the cells were allowed to progress through S phase to mitosis. Samples were mounted in Opti-MEM and time-lapse imaging of the intrinsic GFP was performed after 7 h, when cells began entering mitosis, using an Olympus Fluoview 1000 with a 60X NA 1.42 objective.
description: 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/j05m65t9
title: CIL:40252, Rattus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of a 1 month old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow. 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.
description: Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) and a 60x oil objective (NA 1.4).
description: Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
DOI: 10.6075/j0959gzq
title: CIL: 50687, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. In Cell Image Library

description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
1.8_Cell_1_MATLAB_Volume_Analysis_Results is a compressed (zipped) folder containing all files required to execute the MATLAB volume analysis. Folder also includes the resulting output files and figures.
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: 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: 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
DOI: 10.6075/j0hh6k68
title: CIL:40235, Mus musculus, CNS neuron (sensu Vertebrata), glial cell, blood vessel endothelial cell. In Cell Image Library

description: The animal was perfused with Ringer's solution for 2 minutes followed by DiI for 10 minutes, and then 2% paraformaldehyde for 10 minutes. The brain was post-fixed overnight, and the tissue subsequently sectioned. After buffer washes, sections were stained with Fluoromyelin (1:100 overnight in cold room), rinsed with buffer washes, and subsequently stained TO-PRO3 (1:3000) for 45 minutes at room temp, rinsed and mounted using Gelvatol. 16 z-planes at 5 µm intervals across the entire section used to generate the tiled 3-D mosaic, acquired with an Olympus Fluoview 1000.
description: Coronal section of rat brain triple-labeled with fluoromyelin (green), DiI (red), and TO-PRO3 (blue) which stain for myelin, blood vessels, and cell bodies, respectively. A maximum projection image was compiled by acquiring images across the entire rat brain section, and through 16 optical sections spanning the thickness of the section. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. It is also available through the Whole Brain Catalog (http://wholebraincatalog.org).
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: differences in adsorption or binding of stain; compartmentalization of stain or label
Visualization methods: DiI; fluorescent labels
Data qualification: Processed
DOI: 10.6075/j0n58mh8
title: CIL:40234, Mus musculus, CNS neuron (sensu Vertebrata), glial cell, blood vessel endothelial cell. In Cell Image Library

description: Coronal section of rat brain triple-labeled with fluoromyelin (green), DiI (red), and TO-PRO3 (blue) which stain for myelin, blood vessels, and cell bodies, respectively. A maximum projection image was compiled by acquiring images across the entire rat brain section, and through 16 optical sections spanning the thickness of the section. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. It is also available through the Whole Brain Catalog (http://wholebraincatalog.org).
description: The animal was perfused with Ringer's solution for 2 minutes followed by DiI for 10 minutes, and then 2% paraformaldehyde for 10 minutes. The brain was post-fixed overnight, and the tissue subsequently sectioned. After buffer washes, sections were stained with Fluoromyelin (1:100 overnight in cold room), rinsed with buffer washes, and subsequently stained TO-PRO3 (1:3000) for 45 minutes at room temp, rinsed and mounted using Gelvatol. 16 z-planes at 5 µm intervals across the entire section used to generate the tiled 3-D mosaic, acquired with an Olympus Fluoview 1000.
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: differences in adsorption or binding of stain; compartmentalization of stain or label
Visualization methods: DiI; fluorescent labels
Data qualification: Processed
DOI: 10.6075/j0wq03x3
title: CIL:40227, 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 25th 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/j0dn44q9
title: CIL: 53524. In Cell Image Library

description: AGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j0571c5k
title: CIL:40225, 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: 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 7th 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/j09023xb
title: CIL:40224, 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 26th 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/j0jq10dd
title: CIL: 50686, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. In Cell Image Library

description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
1.7_Cell_1_Surface_Rendering is a compressed (zipped) folder containing all files required to render the surface of the bundle. Also included is the ‘ProjectLog’ file produced by Slice and View acquisition software.
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
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.
DOI: 10.6075/j0hm58k4
title: CIL:40221, 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 4th 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/j04749md
title: CIL: 50682, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. In Cell Image Library

description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
1.3_Cell_1_Stack_Cropped is a multipage TIFF file containing only the relevant volume of Cell#1, cropped to reduce the file size. The file contains 387 images, acquired at 15 nm milling step, resulting in 2.43×2.43×15 nm³ voxel size. The plane #1 of the original stack was removed.
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
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.
DOI: 10.6075/j0td9xgw
title: CIL:40240, Rattus norvegicus, CNS neuron (sensu Vertebrata). In Cell Image Library

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.
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 40X N.A. 1.3 oil-immersion objective. 147 x 60 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
DOI: 10.6075/j0z31zr0
title: CIL:40238, Mus musculus, CNS neuron (sensu Vertebrata), glial cell, blood vessel endothelial cell. 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: differences in adsorption or binding of stain; compartmentalization of stain or label
Visualization methods: DiI; fluorescent labels
Data qualification: Processed
description: The animal was perfused with Ringer's solution for 2 minutes followed by DiI for 10 minutes, and then 2% paraformaldehyde for 10 minutes. The brain was post-fixed overnight, and the tissue subsequently sectioned. After buffer washes, sections were stained with Fluoromyelin (1:100 overnight in cold room), rinsed with buffer washes, and subsequently stained TO-PRO3 (1:3000) for 45 minutes at room temp, rinsed and mounted using Gelvatol. 16 z-planes at 5 µm intervals across the entire section used to generate the tiled 3-D mosaic, acquired with an Olympus Fluoview 1000.
description: Coronal section of rat brain triple-labeled with fluoromyelin (green), DiI (red), and TO-PRO3 (blue) which stain for myelin, blood vessels, and cell bodies, respectively. A maximum projection image was compiled by acquiring images across the entire rat brain section, and through 16 optical sections spanning the thickness of the section. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. It is also available through the Whole Brain Catalog (http://wholebraincatalog.org).
DOI: 10.6075/j0q52prk
title: CIL:40236, Mus musculus, CNS neuron (sensu Vertebrata), glial cell, blood vessel endothelial cell. In Cell Image Library

description: Coronal section of rat brain triple-labeled with fluoromyelin (green), DiI (red), and TO-PRO3 (blue) which stain for myelin, blood vessels, and cell bodies, respectively. A maximum projection image was compiled by acquiring images across the entire rat brain section, and through 16 optical sections spanning the thickness of the section. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. It is also available through the Whole Brain Catalog (http://wholebraincatalog.org).
description: The animal was perfused with Ringer's solution for 2 minutes followed by DiI for 10 minutes, and then 2% paraformaldehyde for 10 minutes. The brain was post-fixed overnight, and the tissue subsequently sectioned. After buffer washes, sections were stained with Fluoromyelin (1:100 overnight in cold room), rinsed with buffer washes, and subsequently stained TO-PRO3 (1:3000) for 45 minutes at room temp, rinsed and mounted using Gelvatol. 16 z-planes at 5 µm intervals across the entire section used to generate the tiled 3-D mosaic, acquired with an Olympus Fluoview 1000.
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: differences in adsorption or binding of stain; compartmentalization of stain or label
Visualization methods: DiI; fluorescent labels
Data qualification: Processed