cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0xw4jv4
title: CIL:10267, Rattus, multipolar neuron. In Cell Image Library

description: Early stages of dendritic development and synapse formation in cultured hippocampal neurons. This multilayer image shows neurons fixed at 7 days in vitro and immunostained for the dendritically localized protein MAP2 (green) and the presynaptic vesicle protein Synapsin I (red). Unstained axons in the field are evident in the phase channel, which is hidden but can be turned on in the viewer. Neurons at 3, 5 and 7 days in vitro are represented in this image group. 

Detailed methods: 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, warmed to 37°C prior to fixation, 15 minutes), permeabilized with 0.25% Triton (7 minutes) and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500; suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j05h7fp5
title: CIL: 50902, Saccharomyces cerevisiae (baker's yeast, budding yeast) Caenorhabditis elegans (roundworm, nematode) Human mast cell line (HMC-1), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Saccharomyces cerevisiae cells were high pressure frozen and embedded in HM20 resin. Samples were then stained for Nuclear Pore Complex (NPC) assosiated proteins with the monoclonal antibody ab24609 (Abcam) and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events. The black gold particles represent the presence of NPC proteins.
description: Wild type cells were cultured in YPD medium and high pressure frozen in a Wohlwend Compact 3 machine,
 followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. For the immuno-EM, samples were blocked for 2 hours in 1% BSA with 0.1% fish skin gelatine. A 1:50 dilution of the primary antibody ab24609 was used and a 1:150 dilution of the secondary antibody rabbit anti-mouse immunoglobulins (E0433, Agilend/Dako). Another incubation with a 1:70 diluted 10 nm gold-conjugated protein A (E1808, CMC UMC Utrecht) was followed. Finally, samples were post fixed in 2.5% glutaraldehyde for 20 minutes. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead 
citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
DOI: 10.6075/j0vm4c0g
title: CIL: 54139, Homo sapiens, HeLa. In Cell Image Library

description: TK 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: 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.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0h70drb
title: CIL:35853, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc15, a protein kinase involves in cytokinesis. These phase and GFPimages are part of an image group containing CIL 35840-35859. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0g73cbc
title: CIL:31263, Homo sapiens, epithelial cell, renal cell carcinoma. 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: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Fluorescein (FITC); TexasRed
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Immunofluorescence images used to investigate stabilization of microtubules (MTs) by Von Hippel-Lindau tumor suppressor protein (pVHL). VHL-deficient RCC-4 cells with empty vector have a lower alpha-tubulin (MTs; green) signal relative to GSK-3beta (red; an internal fluorescence control), compared with RCC-4 cells expressing pVHL30, suggesting that VHL stabilizes MTs. RCC-4 cells were infected with a retroviral vector to express pVHL30, fixed in 3% paraformaledehyde and permeabilized in 0.2% Triton X-100. Primary antibodies used were: monoclonal anti-GSK3beta and polyclonal anti-alpha tubulin. Secondary antibodies used were: anti-rabbit FITC and anti-mouse Texas-Red. Stacks of 5 z planes were acquired with a Leica SP2 system using the 63x 1.4NA, Oil, HCX Plan-Apo Objective and the distance between z planes is 1 micron. This stack corresponds to J Cell Biol. 2010. 190: 991-1003--Fig 1C (left panels) and the images of RCC-4 expressing pVHL30 are in Fig 1C (right panels) and CIL# 31263.
DOI: 10.6075/j04t6hqv
title: CIL:38671, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and cation-dependent mannose-6-phosphate receptor (an integral membrane protein that localizes to the trans-Golgi
 reticulum, endosomes, and the plasma membrane; smaller gold particles) staining. Note that trans‚ÄêGolgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to cation-dependent mannose-6-phosphate receptor (rabbit) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0z89bk2
title: CIL:18493, damselfly, flight muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: unembedded tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
description: Most images show fractures through the outer membrane of mitochondria and SR/T tubules of dyads nestled in long grooves of the mitochondrial surface. All leaflets of the membranes appear in the images. This image is part of the group image CFA00512. TEM magnification 24400X. The negative film was scanned at LBL then reduced in size for upload. Scan step size is 6.3 micron, then reduced in size 4X for upload, for an effective pixel size of 25 micron. Technical details: Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer. pH 7.2. stored at 4C for several days. Muscle dissected out. Infiltrated in 30% glycerol in water. Frozen in liquid nitrogen cooled Freon, fractured in Balzers 400 Freeze-fracture, shadowed with platinum at 45o angle. Replicas were cleaned with Clorox (to remove tissue and with either sulfuric acid or NaOH to try removing the tracheolae. Replicas examined in a Philips 410 Microscope. Reference for these images: 
Takekura, H. and Franzini-Armstrong C. The structure of Ca2+ release units in arthropod body muscle indicates an indirect mechanism for excitation-contraction coupling. Biophys. J. 83, 83, 2742-2753, 2002.
DOI: 10.6075/j07d2tr9
title: CIL: 53157, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Image 4, z=19 from SC_030
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j07w6bqd
title: CIL: 52473, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=5, y=1, z=7 from BL32077_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j01g0khb
title: CIL:2172, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 4 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0d21wft
title: CIL:38963, Drosophila, invertebrate nurse cell, oocyte, follicle cell. In Cell Image Library

description: B0003778 Drosophila embryo polarity . Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: In situ hybridizations showing the localization of bicoid (top), oskar (middle) and gurken (bottom) mRNAs in the stage 10 Drosophila egg chambers. These localizations define the anterior- posterior and dorsal-ventral axes of the embryo. The egg chambers consists of 15 nurse cells and a large oocyte (right), which is surrounded by a layer of somatic follical cells. Bicoid mRNA localises to anterior of the oocyte, directing where head and thorax of embryo develop. Posterior localisation of oskar mRNA directs formation of the pole plasm that contains the abdominal and germline determinants. Gurken is translated on the dorsal side, producing a signalling molecule that causes adjacent follical cells to define the embryo's dorsal-ventral axis.
description: Preparation: in situ hybridization
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: differences in adsorption or binding of stain; boundaries between regions with different refractive index
Source of contrast: optical path length gradient; absorption of illumination
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed
DOI: 10.6075/j0sq8z5p
title: CIL:40558, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: To label membranes inside the cell we used very lightly fixed cells (0.25% glutaraldehyde) that were then rapidly frozen in liquid nitrogen and sectioned later at -100oC. These frozen sections were picked up on drops of methylcellulose and transferred to a Formvar-supported grid. The sections were immunogold labeled (15nm gold) to show the location of the specific antigen inside the cell as well as on the cell surface. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: At the same time that the acidosomes fuse with the phagosome, the DV-I membrane, that originated from the discoidal vesicles, is transformed into tubules that are removed from the phagosome. By this process the DV-I is transformed from a phagosome into a phagoacidosome (DV-II), a process of apparently ‚Äútotal‚Äù membrane replacement. (For discussion see Allen et al., J. Cell Sci. 108:1263-1274, 1995). The mAb to antigen Q2 specifically labels the tubules that are being removed from the DV-I. TEM taken on 9/18/93 by R. Allen with Zeiss 10A TEM. Neg. 12,000X. Part published in J. Cell Sci. 108:1263-1274, 1995. Adapted with permission.
DOI: 10.6075/j0765dcg
title: CIL:2825, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j09k49jh
title: CIL:39578, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Data qualification: Raw;spatialmeasurements
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc15, a protein kinase involves in cytokinesis. These phase and GFP z-series images are part of an image group containing CIL 39576-39580. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j0wh2p89
title: CIL:346, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Thin section electron microscopy of gastrocnemius (skeletal) muscle from a wild type mouse.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 20,000X magnification.

This image is part of a set of wild type gastrocnemius muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data