cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0445ks9
title: CIL:39319, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The infraciliary lattice in this quick-freeze deep-etched image consists of a meshwork of branching fibers composed of many subfibers. Basal bodies and trichocyst tips extend through the openings of the mesh. Individual metal-coated fibrils of the mesh average 11 nm in diameter and are closely interlaced and cross-linked to other fibrils. TEM taken on 5/27/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 9,780X. 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: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0d799d3
title: CIL:36246, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: 11 micrographs of views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows 4 food vacuoles. The helically contracted stalk is seen in cross section through the first turn of the helix. Lateral margins of the trochal band of basal bodies. Body myonemes converge aborally where they will enter the stalk. TEM taken on 4/9/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 2,400X. Bar = 2µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39328) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0xw4j0x
title: CIL:12915, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

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: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets, as indicated by peripheral labeling with adipophilin (smaller gold particles) and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein) staining (larger gold particles). Note that trans‐Golgi 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: 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 adipophilin (guinea pig anti-adipophilin) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (15 nm anti-mouse, 10 nm anti-guinea pig; 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 11,500 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0hx1cdq
title: CIL: 54217, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TKL 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.
DOI: 10.6075/j0pk0f37
title: CIL:36116, damselfly, flight muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
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
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
description: Longitudinal and cross sections showing ribbon like myofibrils regularly alternating with layers of mitochondria and SR/T tubules. Dyads are located in a grove of the mitochondrial surface. Negatives aere scanned on nikon 8000 at 4000dpi/6.3 micron scan step size, 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 (pH7.2). Stored at 4C for several days. Muscle dissected out. Rinsed 3Xin buffer, postfixed in 2% PsO4 in buffer, for 1.5 hrs; rinsed 3 times in water, en-block stained in saturated aqueous uranyl acetate, embedded in Spurr. Thin sections stained in uranyl acetate and lead and examined in a Philips 410 Microscope.
 
 Reference for the image:
Loesser, K.E., Castellani, L. and Franzini-Armstrong, C. Disposition of junctional feet in muscles of invertebrates. J. Muscle Research Cell Motility 13:161-173, 199
DOI: 10.6075/j0vm4bdf
title: CIL:12350, 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of the somatic basal bodies along the sides of the cytoproct ridge have bundles of microtubules extending into the endoplasm from near their proximal ends. These bundles make contact with the spent vacuole and aid its movement to the cytoproct. The plasma membrane and alveolar sacs were ruptured in this cell during preparation for electron microscopy. TEM taken on 6/13/79 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 10,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0154gjz
title: CIL: 52320, 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: One z layer of a z-stack at the given tile position
description: Tile x=5, y=2, z=1 from BL_024216_Myc_Terc
DOI: 10.6075/j0hq3zbj
title: CIL: 51260, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j0hm57p2
title: CIL:1179, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. 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: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j0sx6c2m
title: CIL:11643, Carassius sp. U8MN, saccular macula. 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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Figure 327 from Chapter 13 (Cilia and Flagella) of 'The Cell' by Don W. Fawcett M.D. Longitudinal section of the apex of a hair cell from the saccular macula of the goldfish. The stereocilia are seen in longitudinal section, the sensory hairs are narrower at their base and contain a large number of parallel filaments that converge into a dense bundle in the narrow basal region of the hair and then diverge again as they continue into the cuticular plate in the apical cytoplasm. A copy of the chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0r49q33
title: CIL:39251, Didinium nasutum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Didinium nasutum showing the two prominent girdles of cilia in full metachronous beat. If you look at higher magnification you will see the occasional short, blunt clavate cilia. These are known to not contain central microtubules. (See Wessenberg, H. and Antipa, G. Studies on Didinium nasutum. I. Structure and ultrastructure. Protistologica 4:427-447). Also this specimen represents an early divider, and just anterior to the posterior girdle of cilia, the presumptive clevage furrow can be seen at higher magnification (See Small, E. B., Antipa, G. A. and Marszalek, D. The cytological sequence of events in the binary fission of Didinium nasutum (O. F. M.). Acta Protozool. 9:275-282). This micrograph was taken in 1968 by G. Antipa on a Cambridge Mark IIA operating at 20kV. The negative magnification is 842X. Further details are available at Wessenberg, H. and Antipa, G. 1970. Capture and ingestion of Paramecium by Didinium nasutum. J. Protozool. 17:250-270.
description: Preparation: chemically fixed tissue; lyophilized specimen; Parducz fixative; Au/Pd metal sputter-coat
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: illumination by electrons; secondary_electron imaging
Parameter imaged: illumination by electrons; secondary electron generation; secondary_electron imaging
Source of contrast: detection of electrons
Visualization methods: shadowing and plating
Processing history: recorded image; film
Data qualification: Raw
DOI: 10.6075/j0jw8d1t
title: CIL:12060, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, 0.5 micrometer sections prepared, and stained with uranyl magnesium acetate. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this low magnification survey micrograph of chromosomes at anaphase, the grid was tilted to 70 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j03n22k4
title: CIL:13156, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A tangential section of basal body pair (dikinetid) showing a connecting fiber linking the BBs as well as attachments to a kinetodesmal fiber, to postciliary microtubules, and to transverse microtubules. TEM taken on 2/21/69 by R. Allen with Philips 300 operating at 60kV. Neg. 47,100. Bar = 0.1µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12067) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0h1316p
title: CIL:13180, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, 0.5 micrometer sections prepared, and stained with uranyl magnesium acetate. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of chromosomes at anaphase, the grid was tilted to 45 degrees. A similar micrograph tilted to 55 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j08p60nm
title: CIL:40072, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with either 5% aqueous LY in 200 mM KCl. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were then ready to be immunolabeled. The rabbit anti-EphA4 antibody was provided by Dr. Elena Pasquale (The Burnham Institute, La Jolla, CA). EphA4 was subsequently detected using goat anti-rabbit Cy5. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
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: intracellular filling; distribution of epitope
Visualization methods: lucifer yellow; primary antibody plus labeled secondary antibody; Cy5
Data qualification: Processed