cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j04b2zxk
title: CIL:39081, Triticum sp., leaf. In Cell Image Library

description: Leaf segments 1 cm from the tip were fixed with 2% glutaraldehyde, postfixed with 1% osmium tetroxide, dehydrated, and embedded in Spurrs resin. Thin sections were stained with uranly acetate and lead citrate and examined in a JEOL 100C transmission EM at 60 KV, and images recorded on film. See Fig 7 in K D Allen et al. 1988 Biogenesis of thylakoid membranes is controlled by light intensity in the conditional chlorophyll b-deficient CD3 mutant of wheat. J Cell Biol 107:907-919
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Data qualification: Processed
description: CD3 mutant wheat (deficient in chlorophyll b) was germinated and grown for 6 days in the dark, greened at low light intensity for 4 days, then prepared for thin section electron microscopy. Under these conditions, the mutant chloroplast shows the characteristic grana stacks of thylakoids (GT) and unstacked stromal regions (ST). Also seen are osmiophilic globules (PG). This set of grouped images, which also shows freeze-fracture views, includes chloroplasts from wild type wheat.
DOI: 10.6075/j0dj5d9k
title: CIL:39080, Triticum sp., leaf. In Cell Image Library

description: CD3 mutant wheat (deficient in chlorophyll b) was germinated and grown for 6 days in the dark, greened at high light intensity in the presence of chloramphenicol for 4 days, thylakoids prepared, plunge-frozen, and freeze-fracture replicas obtained and examined by transmission electron microscopy. This region shows the characteristic particle size and distribution found on the EFs and PFs membrane faces of stacked thylakoid membranes. This set of grouped images, which also shows thin sections, includes images of wild-type wheat.
description: Thylakoid preparations were equilibrated with 35% glycerol, plunge frozen in liquid Freon 12 cooled in liquid N2 and fractured and replicated in a Balzers BA 360 freeze etch device. Replicas were examined in a JEOL 100C at 80KV and images recorded on film. See Fig 13 in K D Allen et al. 1988 Biogenesis of thylakoid membranes is controlled by light intensity in the conditional chlorophyll b-deficient CD3 mutant of wheat. J Cell Biol 107:907-919.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
DOI: 10.6075/j0mc8xp0
title: CIL:39078, Triticum sp., leaf. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Data qualification: Processed
description: Leaf segments from mutant plants taken 1 cm from the tip were fixed with 2% glutaraldehyde, postfixed with 1% osmium tetroxide, dehydrated, and embedded in Spurrs resin. Thin sections were stained with uranly acetate and lead citrate and examined in a JEOL 100C transmission EM at 60 KV, and images recorded on film. See Fig 6 in K D Allen et al. 1988 Biogenesis of thylakoid membranes is controlled by light intensity in the conditional chlorophyll b-deficient CD3 mutant of wheat. J Cell Biol 107:907-919
description: Mutant CD3 wheat seeds (deficient in chlorophyll b)were germinated and grown for 6 days in the dark, greened at high light intensity for 4 days, then prepared for thin section electron microscopy. CD3 chloroplasts have mostly unstacked thylakoid membranes. Also seen are semi-crystalline arrays (arrowhead) and membrane whorls (Wh and inset). This set of grouped images, which also shows freeze-fracture views, includes wildtype chloroplasts.
DOI: 10.6075/j0n29vrn
title: CIL:39076, pancreatic cancer cell. In Cell Image Library

description: B0007252 Pancreatic cancer cells. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Relation to intact cell: dispersed cells in vitro
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: visualization of contiguous regions
Processing history: colorized
description: A colorized scanning electron micrograph of pancreatic cancer cells grown in culture. See additional image at CIL: 39104.
DOI: 10.6075/j0tt4ptq
title: CIL:39064, hair follicle cell, sweat secreting cell. In Cell Image Library

description: Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: modes of light microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Processing history: unprocessed raw data
description: B0007564 Scalp. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Light micrograph of a section cut through the dermis of the scalp. The dermis is the lower (or innermost) layer of the that makes up the skin; the other layer is the epidermis. The dermis contains hair follicles, sweat glands, sebaceous glands, blood vessels and lymph vessels. The section is cut tangentially in a plane +/- parallel to the skin surface. Hair follicles (blue and bright red circles) are seen in transverse sections on the left hand side, sebaceous glands are shown as pink masses ,and groups of sweat ducts are seen as patches of small dark blue circles, all of which are embedded in a matrix of blue collagen fibers. The right hand side is dominated by adipose tissue (fat), as white spaces among which are scattered hair follicles and groups of sweat glands.
DOI: 10.6075/j0x63krx
title: CIL:39060, osteoblast. In Cell Image Library

description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); phalloidin; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Processing history: unprocessed raw data
description: Confocal micrograph of osteoblast cells labeled with Alexafluor 488 that stains alpha tubulin (green) and phalloidin marking the actin (purple) and DAPI highlighting the nucleus (yellow). Osteoblasts originate in bone marrow and contribute to the production of new bone. These cells build up the matrix of bone structure and as bone is continually being reabsorbed and regenerated these are very crucial cells. Osteoblasts make up bone and osteoclasts break it down.
description: B0007570 Osteoblasts. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0gq6wm4
title: CIL:39058, neuron of the dorsal spinal cord. In Cell Image Library

description: B0007573 Dorsal root ganglion. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: This confocal micrograph shows a dorsal root ganglion (DRG) explant. The dorsal root ganglion is a swelling on the dorsal roots of spinal nerves, which contains a cluster of cell bodies and synapses. In vertebrates the dorsal root ganglia lie outside the central nervous system. The DRG shown here has been visualized by staining with TRITC-phalloidin to highlight actin (red) and neurofilaments (green).
description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: explant
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin; Tetramethyl rhodamine (TRITC); primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j09885wr
title: CIL:39057, blood cell. In Cell Image Library

description: 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
description: B0007588 Blood clot. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Colorized scanning electron micrograph of the components of a blood clot. Clotting of the blood is an important process that helps the body repair after injury. The blood is composed of red blood cells, which carry oxygen (shown in red), white blood cells that help fight infection (not present in this image) and platelets that are crucial in the clotting process. Platelets travel to the injured area to form a plug. Once there, they are involved in activating clotting factors, the main one being fibrin. Fibrin is a protein that crosslinks with itself to form a mesh that makes up the final blood clot (shown in this image as a string-like mesh). A blood clot is also known as a thrombus and if a thrombus occurs when it is not required it can have serious medical consequences, such as a stroke or heart attack.
DOI: 10.6075/j01835b6
title: CIL:39071, Populus, ray cells. In Cell Image Library

description: B0007535 Microfilaments. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
description: This confocal image shows microfilaments (in green) and cell nuclei (in red) of developing wood cells in poplar. In plants, the cytoskeleton is specialised for particular functions. This image shows the cells that will increase in length to run from the outside of the tree's trunk towards the inside (the ray cells, which are observed looking like the spokes of a wheel looking down at a cut tree stump) along with other cells that will increase in length parallel to trunk. In both cases the direction of cell extension is mirrored by the arrangement of the microfilaments.
DOI: 10.6075/j0959gf0
title: CIL:39069, Mus musculus, motor neuron. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of epitope
Visualization methods: EGFP; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: B0007552 Mouse forelimb motor neuron development 11.5 days post coitum. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Confocal micrograph showing the development of motor neurons in the mouse forelimb at 11.5 days post coitum. The transgenic mice expresses a transgene of the Hb9 gene containing a genetic insert of the gene expressing green fluorescent protein (GFP). This transgenic insert allows the growth of motor neurons to be tracked. GFP is expressed where ever Hb9 is expressed and can be visualized using fluorescent immunohistochemistry techniques. This method can be used to accurately the time the motor neurons enter the limb to the point when they have branched to innervate all the developing muscles. In this image the developing motor neurons are shown in green (anti-GFP) and the muscle (myosin-32) is shown in red.
DOI: 10.6075/j0f47n0c
title: CIL:39068, sperm, duct epithelial cell, smooth muscle cell. In Cell Image Library

description: Light micrograph of a longitudinal section of the epididymis. The lining of the duct consists of pseudostratified epithelial cells, which have prominent microvilli on their free surface extending into the lumenal space that contains the spermatozoa. Around the epithelial cells is a layer of smooth muscle, which propels the spermatozoa outwards along the duct during ejaculation. Thousands of spermatozoa are present in the epididymis (the sperm heads are visible as dark spots in the central luminal space) and they are stored here after being produced in the seminiferous tubules of the testis. The cells seen among the spermatozoa are probably lymphocytes. This is a 1.5um (semithin) section stained with haematoxylin and eosin (H+E).
description: B0007559 Primate epididymis. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: hematoxylin; eosin
Processing history: unprocessed raw data
DOI: 10.6075/j0f18xkn
title: CIL:39067, Eudorina, colonial green algae. 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
Processing history: unprocessed raw data
description: Nomarski differential interference contrast image of Eudorina. Eudorina consist of either 16, 32 or 64 (mostly 32) cells embedded in a spherical mass of gelatinous material. Each cell contains a chloroplast (giving them a green color), a red eyespot and two flagella. Eudorina are a free-swimming colonial green algae commonly found in ponds and farm puddles, usually in sufficient concentrations to make the water green.
description: B0007560 Eudorina (green algae). Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0fq9w0w
title: CIL: 50712, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 4.9_Cell_4_MATLAB_Volume_Analysis_Results. 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. 
4.9_Cell_4_MATLAB_Volume_Analysis_Results is a compressed (zipped) folder containing all files required to execute the MATLAB volume analysis. The folder also includes the resulting output files and figures.
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: 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
DOI: 10.6075/j09z948j
title: CIL: 50711, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 4.8_Cell_4_Surface_Rendering. 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. 
4.8_Cell_4_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 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: 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
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/j01g0mdd
title: CIL:40233, Rattus norvegicus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: The PMCA1a antibody (CR1a) was generated by immunizing New Zealand rabbits with keyhole limpet hemocyanin-conjugated synthetic peptide (Filoteo et al., 1997). NR1a was generated against a 20-residue peptide sequence (VFSSSTASTPVGYPSGECIS, residues 37-57) in the carboxy terminus region of the rat PMCA1a. The specificity of NR1a was established by western blots using microsomes from COS cells overexpressing specific PMCAs, and further confirmed in microsomes from rat brain. CR1a recognizes only one band at 129 kDa. Staining was absent in the presence of the peptide immunogen.

Tissue Preparation

All procedures related to the care and treatment of animals were in accordance with institutional and NIH guidelines. Twelve male Sprague-Dawley rats (200-350 g, Charles River, Raleigh, NC) were used for this study. After inducing deep anesthesia with sodium pentobarbital (60 mg/kg, i.p.), rats were intracardially perfused with heparinized saline followed by 500 ml of fixative. Rats were fixed with 4% paraformaldehyde freshly-depolymerized in phosphate buffer (PB, 0.1 M, pH 7.4). Brains were then removed and postfixed 2 h at 4 degrees C in the same fixative. Brains were cut at 40-60 ¿m on a Vibratome and collected in cold PB.

Light microscopy
Free-floating sections were permeabilized with 50% ethanol for 30 min and then treated for 30 min with 3% H2O2 in phosphate-buffered saline (PBS, 0.1 M, pH 7.4). After preincubation in 10% normal donkey serum (NDS, to block secondary antibody binding sites), sections were incubated in CR1a (1:1,000) overnight on a shaker at room temperature. For immunoperoxidase microscopy, sections were then incubated for 3 hours in biotinylated secondary antibody (1:200; Jackson ImmunoResearch, West Grove, PA) and for 1 hour in ExtrAvidin-peroxidase complex (1:5,000; Sigma, St. Louis, MO); peroxidase was histochemically visualized with diaminobenzidine. Processed sections were mounted on gelatin-coated slides, air dried, and cleared with xylene before being coverslipped with D.P.X. mountant (BDH Chemicals, Poole, England).
description: Large scale mosaic of a 40 um thick parasagittal section of rat brain immunolabeled with against the plasma membrane calcium pump protein, PMCA1a, using a polyclonal antibody against the C terminus and peroxidase-DAB as the chromagen. 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) Cellular and subcellular localization of PMCA1a in the rat brain. J. Comp. Neurol. PMID 20575074.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: modes of light microscopy
Parameter imaged: distribution of epitope
Visualization methods: biotin; primary antibody plus labeled secondary antibody
Data qualification: Processed
DOI: 10.6075/j09c6xjn
title: CIL:40247, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
Parameter imaged: electron density
Data qualification: Processed
description: Single slice from a serial section series through the mouse retina taken with serial block face SEM. 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/j0h41rkk
title: CIL:40258, Rattus norvegicus, peripheral neuron. In Cell Image Library

description: Chemical fixation with 2% paraformaldehyde and 2.5% glutaraldehyde via vascular perfusion in 0.15M cacodylate buffer (pH 7.4) at 37 degrees C followed by high pressure freezing and freeze substitution using a Bal Tec HPM010 high pressure freezer (from Perkins et al., J. Structural Biology 161, 469, 2008).
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: A single image from animation of the computed slices through a tomographic volume of mitochondria at the Node of Ranvier in rat peripheral nerve root. 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: Perkins et al. Mitochondrial configurations in peripheral nerve suggest differential ATP production. J. Struct. Biol. (2010), doi:10.1016/j.jsb.2010.06.017 http://www.ncbi.nlm.nih.gov/pubmed/20600951