cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0zw1k83
title: CIL:39316, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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
description: A row of large IMPs bordering parts of the plates are visible. Two parentheses-shaped empty trichocyst docking sites are also present and one ring surrounding pits where the rosette IMPs have been removed. TEM taken on 5/9/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800. 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/).
DOI: 10.6075/j0ms3sb3
title: CIL: 52738, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
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=4, y=3, z=20 from PS11_10021_2B_Myc_Terc
DOI: 10.6075/j0cf9pqf
title: CIL: 53374, Homo sapiens, HeLa. In Cell Image Library

description: CAMK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j09z94db
title: CIL: 52022, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
DOI: 10.6075/j0b56jr1
title: CIL:35689, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP taggedMAD2. 
 
MAD2 is a non-essential gene that encodes a component of the spindle checkpoint. The spindle checkpoint delays the onset of anaphase in cells with defects in mitotic spindle assembly or in the attachment of chromosomes to the spindle microtubules. The checkpoint works by inhibiting the activity of the anaphase promoting complex, thereby preventing the degradation of several cell cycle regulators. Like other spindle checkpoint mutants, mad2 loss-of-function mutants are sensitive to benomyl and cannot delay cell division in response to spindle depolymerization. Mad2p forms a tight complex with another spindle checkpoint protein, Mad1p, throughout the cell cycle. Mad2p also forms a complex with Cdc20p, which activates the anaphase promoting complex, and Mad3p; the presence of Mad1p is required for the complex to form. Bub1p, Bub3p, Mad1p, Mad2p, Mad3p, and the protein kinase Mps1p act in a branch of the spindle checkpoint pathway that may prevent premature chromosome disjunction. A second branch involves Bub2p and Bfa1p, and may prevent cytokinesis prior to chromosome segregation. Homologs of Mad2p act in the spindle checkpoint in Xenopus (Xmad2) and human (MAD2L1 andMAD2L2.MAD2 was originally identified as the open reading frame YJL031C. However, it is now known thatMAD2 corresponds to the adjacent open reading frame YJL030W, while YJL031C encodes the geranylgeranyltransferase subunit Bet4p.
 
These phase,gfp images are part of an image group that ranges from CIL:35680-35699. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors 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
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
DOI: 10.6075/j0bk1bfr
title: CIL:9812, Opercularia [NCBITaxon:168247], Opercularia coarctata, 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; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: A contractile vacuole in systole. The CV has collapsed into vesicles and tubules. Three CV pores can be seen where the CV meets the pellicle. Smooth membrane cisterna surrounds some cytoplasm, possibly a developing stage of an autophagic vacuole. TEM taken on 6/12/69 by R. Allen with Philips 300 operating at 60kV. Neg. 9,250X. Bar = lµm. A print of the negative was scanned and processed in Photoshop. This image is suitable for qualitative analysis. There is a high resolution version of this image in the library (CIL:39335) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.
DOI: 10.60686/t-fsd3902
title: FSD3902 National Library's Digital Resources and Services: Researcher Survey 2024
DOI: 10.6075/j0028qcs
title: CIL:23038, Rattus, fibroblast. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; tannic acid
Relation to intact cell: platinum replica
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: uranyl salt; shadowing and plating; primary antibody plus labeled secondary antibody; immunogold
Processing history: unprocessed raw data
description: An REF-52 cytoskeleton with actin filaments decorated by myosin S1. An intermediate filament associates with an actin filament bundle via plectin sidearms (10-nm immunogold labeling). Electron microscopy of cytoskeletons was performed as described (Svitkina et al., 1995). Briefly, cells on coverslips were lysed as for light microscopy, treated, with recombinant gelsolin NHz-terminal domain, fixed with glutaraldehyde, tannic acid and uranyl acetate, critical point dried, and coated with platinum and carbon. Image corresponds to Fig 10a from J Cell Biol. 1996 Nov;135(4):991-1007. Image corresponds to Fig 10a in J Cell Biol. 1996 Nov;135(4):991-1007.
DOI: 10.6075/j0mk6d1k
title: CIL:40170, 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 Alexa 568. 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 immunostained and 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 astrocytes.
description: Projection through merged optical section series of adjacent hippocampal astrocytes from a 1-week old male rat, injected with Lucifer Yellow (green) and Alexa568 (red) respectively, and immunolabeled for GFAP (blue), imaged with confocal microscopy. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86. 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: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Data qualification: Processed
DOI: 10.6075/j0xg9qg1
title: CIL:43552, Allium cepa, root tip. In Cell Image Library

description: Acetocarmine stained root tips were viewed with a bright field light microscope using a 40x 0.65 N.A. objective lens, and recorded on film.
description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: film
Imaging mode: modes of light microscopy
Parameter imaged: compartmentalization of stain or label
Source of contrast: differences in adsorption or binding of stain
Visualization methods: acetocarmine
Data qualification: Processed;spatialmeasurements
description: Light micrograph of onion (Allium cepa) root tip cells stained with acetocarmine to show nuclei and chromosomes. The field includes cells in interphase, prophase, metaphase, and late telophase.
DOI: 10.60686/t-fsd4006
title: FSD4006 Citizens' Pulse: Combined Data 2023
DOI: 10.6075/j0hd7ttk
title: CIL:9805, Euplotes sp., 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
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;intensitiesquantitation
description: A high resolution micrograph of the proximal ends of the basal bodies of a cirrus of Euplotes. the basal bodies are embedded in a perforated plate of electron opaque material. Microtubules arise from this opaque material and a secondary fretwork of connections binds the basal bodies midway along their length. ves, vesicles. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 7/24/67 by R. Allen with Philips 200 operating at 60kV. Neg. 12,400X. The raw negative was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j05m648q
title: CIL:48766, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 6
 
Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j008643g
title: CIL:40501, Paramecium multimicronucleatum, 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. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: Enlargement of two mitochondria showing the cross sections of tubular cristae bear one pair of protrusions (these are the F1 subunits of F1F0 ATP synthase enzymes) while rows of protrusions can be viewed along some tangentially sectioned tubules. The tubules in some cases can be seen to arise from the inner membrane. TEM taken on 3/7/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 22,500X. 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/).
DOI: 10.6075/j0th8kdh
title: CIL:11623, Rattus sp., tracheal epithelial cell. In Cell Image Library

description: Abstracted from an image by Simionescu and Simionescu in The Journal of Cell Biology (70:608-621), ©1976, The Rockefeller University Press. This image was reprinted as Figure 319 from Chapter 13 (Cilia and Flagella) 'The Cell' by Don W. Fawcett M.D.(1981, W.B. Saunders Company). Ciliated cells of mammals often have microvilli interspersed among the cilia. These transverse sections near the cell surface permit a comparison of the size and internal structure of the two types of cell process. Both are limited by a trilaminar unit membrane and have a cytoplasmic matrix of similar density. The nonmotile microvilli have no resolvable internal structure, whereas the motile cilia have a consistent pattern of nine doublet microtubules uniformly spaced around a central pair of singlet microtubules. This nine plus two complex was visualized by the early light microscopists as a single axial fiber and was therefore called the axoneme. The term has been retained even though it does not accurately describe the microtubule complex revealed by the electron microscope. A copy of Chapter 13 from 'The Cell' is available on the ASCB's BioEDUCATE website.
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; tannic acid
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0m044jc
title: CIL:13157, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Basal bodies are supported by three fiber systems, a striated kinetodesmal fiber that arises from the proximal end of the basal body and curves upward and anteriorly within the longitudinal ridge to the cell's right side of a row of basal bodies. Extending posteriorly and also curving up into the longitudinal ridge is a ribbon of postciliary microtubules. The kd may extend past several more anterior basal bodies but the postciliary ribbon does not extend beyond the next posterior basal body or pair of basal bodies in the kinety. Only the more posterior of the two basal bodies within a single depression is associated with the ends of these two accessory structures. An indentation of the plasma membrane, the parasomal sac, lies to the cell's right of each basal body or pair of basal bodies. TEM taken on 1/5/73 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. Bar = 0.2µm. 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:12068) 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/j0d799n7
title: CIL:1441, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 68,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

stereo pair with CIL:1442
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data