cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0x34xmm
title: CIL:40152, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Tissue came from either mice genetically engineered to overexpress human alpha synuclein (mouse strain, C57BL/6-DBA/2, overexpress a mutant form of alpha synuclein (A53T), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: The neostriatum of a transgenic mouse engineered to overexpress human alpha synuclein under the Thy1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
DOI: 10.6075/j0ht2pf7
title: CIL:40151, Mus musculus, CNS neuron (sensu Vertebrata). 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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: Tissue came from either mice genetically engineered to overexpress human alpha synuclein (mouse strain, C57BL/6-DBA/2, overexpress a mutant form of alpha synuclein (A53T), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: The cerebellar cortex of a transgenic mouse engineered to overexpress human alpha synuclein under the Thy1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
DOI: 10.6075/j0w959bq
title: CIL:40128, Mus musculus, CNS neuron (sensu Vertebrata). 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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: The hippocampal area CA3 of a transgenic mouse engineered to overexpress a mutant form of human alpha synuclein (A53T), immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
DOI: 10.6075/j0c53m05
title: CIL:40127, Mus musculus, CNS neuron (sensu Vertebrata). 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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: The pyramidal cell layer of CA1 from the hippocampus of a transgenic mouse engineered to overexpress a mutant form of human alpha synuclein (A53T), immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
DOI: 10.6075/j0d79bj9
title: CIL:40121, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Wide field brain mosaic of a coronal section of brain from a transgenic mouse engineered to overexpress human alpha synuclein immunolabeled for alpha synuclein (Green) and counterstained with Hoescht 33342 (red) to reveal cell nuclei. The Hoescht staining introduced some non-specific background (red haze). This mosaic image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. For more information regarding this project, see: Price DL, Chow SK, MacLean NAB, Hakozaki H, Peltier S, Martone ME, Ellisman MH (2006) High-Resolution Large-Scale Mosaic Imaging using Multiphoton Microscopy to Characterize Transgenic Mouse Models of Human Neurological Disorders. Neuroinformatics. 2006;4(1):65-80.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Hoechst 33342
Data qualification: Processed
description: Transgenic adult female mouse (624 days, 32 g) was anesthetized with nembutal, and perfused with 4% paraformaldehyde + 0.1% glutaraldehyde, followed by 1 hr. postfixation in 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm. Following rinses in phosphate buffer (PBS), sections were blocked (PBS with 3% NGS;1% fish gel, 0.1% Triton X-1000; 1% BSA) for 1 hour, followed by rinses in working buffer (1:10 blocking buffer: PBS). Primary antibody was diluted in working buffer (anti-alpha-SYN; Host = Rabbit used at 1:500), and tissue was covered with aluminum foil and incubated on a shaker in cold room overnight. Tissue was washed with working buffer and incubated in secondary antibody. After rinses, 1:100 Hoescht 33342 was used to stain nuclei (30 min). After rinsing in PBS, sections were mounted on slides and coverslipped using Gelvatol. Sections were imaged using a BioRad RTS 2000MP Multiphoton, with a 60X, NA 1.4 objective. This tiled image was generated from 57 x 46 (x, y) maximum projection images.
DOI: 10.6075/j0dz07n7
title: CIL:40118, Homo sapiens, HTLV-1 subtype A, mature CD4 single-positive thymocyte, T cell. In Cell Image Library

description: A single computed slice through a tomographic reconstruction of a virological synapse formed between naturally HTLV-1 infected CD4+ T cells and autologous uninfected CD4+ target cells. HTLV-1 particles in the synaptic cleft were identified by immunolabeling using anti-Gag p19 labeling and peroxidase-DAB detection. 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: Majorovits et al. (2008) Human T-Lymphotropic Virus-1 visualized at the virological synapse by electron tomography. PLoS ONE 3: e2251, doi:10.1371/journal.pone.0002251, PMID 18509526
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
description: CD4+ T cells were isolated and cultured overnight to allow spontaneous expression of HTLV-1 proteins, and subsequently prepared for EM. To detect HTLV-1 Gag matrix protein in infected cells the samples were labelled against HTLV-1 Gag p19 (Tanaka et al., 1986) using the DAB kit from Molecular Probes (Invitrogen Ltd, Paisley, UK ). After the PFA/glutaraldehyde fixation, the samples were incubated in PBS containing 1% BSA, 0.1% Triton X-100 and 2% H2O2, for 1 h at 37uC to block non-specific antibody binding and to quench the endogenous peroxidase activity of the cells. To detect the HTLV-1 complexes, the cells were incubated with 5 mg/ml of anti-Gag p19 (GIN7 mAb) [33] diluted in PBS 1% BSA, for 1 h at 37uC. Then the second antibody, anti-Mouse mAb conjugated to HRP (Invitrogen Ltd, Paisley, UK ), was added at a final dilution of 1 mg/ml, and incubated for 30 minutes at 37uC. The cells were washed three times with PBS containing 1% BSA between each step. For detailed methods of the preparation, refer to the CCDB link provided.
DOI: 10.6075/j03n22rc
title: CIL:40112, Mus musculus. In Cell Image Library

description: Zero degree tilt image from a tilt series collected using an intermediate voltage electron microscope through +/- 60 degrees of mitochondria isolated from mouse liver. Section thickness was 0.5 um. 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: For more information see: Yamaguchiet al. Opa1-mediated cristae opening is Bax/Bak and BH3 dependent, required for apoptosis, and independent of Bak oligomerization. Molecular Cell 2008, 31, 557-569.
description: Mitochondria were isolated from mouse liver, incubated with added buffer at 37 degrees C for 12 min in AT buffer containing 10 mM KCl and centrifuged at 5200x g for 6 min, and stored in liquid nitrogen. Preparation was sectioned at a thickness of 5 µm. Single tilt tomogram images were acquired using a JEOL4000EX IVEM, 20,000X, 400.0 kV accelerating voltage, from -60 to 60° at 2° intervals.
description: Relation to intact cell: isolated subcellular component
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
DOI: 10.5281/zenodo.17270970
title: GAS Enn proteins database
DOI: 10.5281/zenodo.17270971
title: GAS Enn proteins database
DOI: 10.6075/j08g8ktk
title: CIL:40122, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Transgenic adult female mouse was anesthetized with nembutal, and perfused with 4% paraformaldehyde + 0.1% glutaraldehyde, followed by 1 hr. postfixation in 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm. Following rinses in phosphate buffer (PBS), sections were blocked (PBS with 3% NGS;1% fish gel, 0.1% Triton X-1000; 1% BSA) for 1 hour, followed by rinses in working buffer (1:10 blocking buffer: PBS). Primary antibody was diluted in working buffer (anti-alpha-SYN; Host = Rabbit used at 1:500), and tissue was covered with aluminum foil and incubated on a shaker in cold room overnight. Tissue was washed with working buffer and incubated in secondary antibody. After rinses, 1:100 Hoescht 33342 was used to stain nuclei (30 min). After rinsing in PBS, sections were mounted on slides and coverslipped using Gelvatol. Sections were imaged using a BioRad RTS 2000MP Multiphoton, with a 60X, NA 1.4 objective. This tiled image was generated from 49 x 44 (x, y) maximum projection images.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Hoechst 33342
Data qualification: Processed
description: Wide field brain mosaic of a coronal section of brain from a transgenic mouse engineered to overexpress human alpha synuclein, immunolabeled for alpha synuclein (green) and counterstained with Hoescht 33342 (red) to reveal cell nuclei. The Hoescht staining introduced some non-specific background (red haze). This mosaic image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. For more information regarding this project, see: Price DL, Chow SK, MacLean NAB, Hakozaki H, Peltier S, Martone ME, Ellisman MH (2006) High-Resolution Large-Scale Mosaic Imaging using Multiphoton Microscopy to Characterize Transgenic Mouse Models of Human Neurological Disorders. Neuroinformatics. 2006;4(1):65-80.
DOI: 10.6075/j0j10391
title: CIL:40126, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: The dentate gyrus of a transgenic mouse engineered to overexpress a mutant form of human alpha synuclein (A53T), immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. 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/j0hd7tfn
title: CIL:40314, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic 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; uranyl salt; lead salt
Data qualification: Processed
description: Transmission electron micrograph of a thin section of the nucleus of a normal HeLa cell showing detail of a cross section of a nuclear pore - from a study of the role of the nuclear porin ALADIN. Other images in this group show additional details of nuclear pore structure in cross section and tangential section.
description: Normal HeLa cells expressing were fixed with glutaraldehyde, embedded in epoxy resin, thin sectioned, and imaged using TEM.
See: J Cronshaw and M Matunis 2003 The nuclear pore complex ALADIN is mislocalized in triple A syndrome Proc Natl Acad Sci USA 100 5823-5827
DOI: 10.6075/j0r78dmr
title: CIL: 50701, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 3.5_Cell_3_GoldParticle_Segmentation. In Cell Image Library

description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
3.6_Cell_3_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 3, comprised of files related to the Cell #3 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 with 10 nm gold beads
DOI: 10.6075/j03f4p13
title: CIL: 50705, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 4.2_Cell_4_Raw_Image_Stack_Part2. In Cell Image Library

description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
4.2_Cell_4_Raw_Image_Stack_Part2 is a multipage TIFF file consisting of an additional 144 EM sections acquired completing the Cell#4. Images were acquired at 15 nm milling step, resulting in 1.95×1.95×15 nm³ voxel size.
This file is a part of Dataset 4, comprised of files related to the Cell #4. The numbering order of the files reflects the order of operations performed during the analysis. Note: The data acquisition session was interrupted after frame #224, and later resumed as a separate imaging session. This resulted in two stack files, concatenated into a single multipage TIFF file during data 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.
DOI: 10.6075/j0ns0t6w
title: CIL:40335, Geranium cinereum, pollen. In Cell Image Library

description: Scanning electron micrograph of Geranium cinereum (geranium) 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: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
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/j0sx6ckb
title: CIL:40333, Paeonia lactiflora, pollen. In Cell Image Library

description: Scanning electron micrograph of Paeonia lactiflora (Chinese) pollen. These peony 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
description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html