cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j01835cn
title: CIL:39511, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The ER tubules in the spasmoneme bear elements of the linkage complex, both the mid piece and rails. These elements are more disperse than in the body of the cell. The fibers from the mid piece pass into the basal bodies of the stalk. TEM taken on 4/9/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 37,750X. Published and adapted with permission from J. Cell Biol. 56:559-579, 1973. 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: 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; Print from negative scanned for Photoshop.
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0rr1xk1
title: CIL:39508, 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: 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;intensitiesquantitation
description: The scopula, stalk-forming region, is outlined by a circle of basal bodies that produce short modified cilia. Other basal bodies lie within this circle. The sheath is secreted outside the circle of cilia. Fibers from linkage complexes enter the proximal ends of these basal bodies. T
 EM taken on 2/24/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. 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/j06d5sbb
title: CIL:39506, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Contractile vacuole pore in face view illustrating the microtubular ribbons that extend from the pore to the CV membrane, the coil of microtubules that surrounds the pore and smaller pellicular pores that appear in the pellicle-bound chamber into which the CV empties. TEM taken on 2/15/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. 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/).
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;intensitiesquantitation
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/).
DOI: 10.6075/j0v69hx0
title: CIL:39505, Vorticella convallaria, 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; Print from negative scanned for Photoshop.
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: The contractile vacuole pore is supported on its cytosolic side by a coil of microtubules and other microtubules extend from the pore to the CV membrane. The plasma membrane and CV membrane cover the bottom of the pore. Bacteria reside in the chamber. TEM taken on 2/14/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. 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/).
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/).
DOI: 10.6075/j09p310p
title: CIL:39744, Mus musculus, retinal rod cell. In Cell Image Library

description: Surface rendered models of chromatin organization from tomogram derived from a TEM image of epon section of a freeze-substituted mouse retina. (C) shows the region boxed in CIL:39743 where 4 regions of chromatin compaction have been outlined. (D) shows sub-volumes interpreted as beads-on-a-string nucleosome arrays. 
 See Fig 2C,D in: C Kizilyaprak et al. 2010. In Vivo Chromatin Organization of Mouse Rod Photoreceptors Correlates with Histone Modifications. PLOS one 5:e11039
description: Item type: portrayed image; computer graphic
Data qualification: Processed
description: See: C Kizilyaprak et al. 2010. In Vivo Chromatin Organization of Mouse Rod Photoreceptors Correlates with Histone Modifications. PLOS one 5:e11039
DOI: 10.15468/dl.6z56rr
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "OccurrenceStatus is Present",
 "TaxonKey is Neofelis nebulosa"
 ]
}

 The dataset includes 20 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009453-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0j9658f
title: CIL:50635, Homo sapiens, monocyte. In Cell Image Library

description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: Imaging mode: microscopy
Visualization methods: x100
description: Monocyte-type cells of elongated form, fibroblast-like, showing nucleus compression by 2 erythrocytes. The erythrocytes seem rather at contact to the cell or superposed and not intracytoplasmic. To note would be a fibroblast-shaped -type cell.
DOI: 10.6075/j06m36c2
title: CIL: 52366, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=2, z=5 from BL024199_Myc_Terc
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
DOI: 10.6075/j03777t3
title: CIL:2728, 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: 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.
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.
DOI: 10.6075/j0qn668v
title: CIL: 52135, 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/j0tx3ddp
title: CIL:7429, Mus musculus, fibroblast, primary cell line cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; saponin permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Alexa Fluor 488; X-Rhodamine; phalloidin
Processing history: unprocessed raw data
description: Image shows (actin polymerization at) free barbed ends and F-actin in the lamellipodium of a migrating primary murine embryonic fibroblast. 
Cell has been mildly permeabilized using saponin during a 2min incubation in cytoskeleton buffer containing X-rhodamine labeled G-actin. Intracellular X-rhodamine actin polymerized into filaments at the very leading edge of the lamellipodium, resulting in the narrow red band along the tip of the lamelipodium. Lamellipodial F-actin was labeled with Alexa488-phalloidin using glutaraldehyde fixation subsequently to the X-rhodamine actin incubation. 
The micrograph visualizes that the actin monomer incorporation into the lamellipodial actin filament structure is restricted to the front of the lamellipodium. This enables a directed extension of the branched actin network towards the plasmamembrane, which pushes the membrane forward thereby creating cell protrusion.

Wide field epifluorescence image taken on using a 100X 1.49 NA lens, Semrock DA/FI/TR/Cy5-4x4M-B Sedat filter set, and an Orca II with 500 ms exposure.
DOI: 10.6075/j0pz57qh
title: CIL:34534, Tetrahymena pyriformis, 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: A high resolution micrograph. Most wild type Tetrahymena have a macronucleus and a micronucleus. The micronucleus, seen here, is essentially nonfunctional during interphase. Its function is to replicate and pass a complete copy of the genome to each daughter cell and to give rise to a new macronucleus following sexual reproduction. Many laboratory strains, unlike strain W which is shown here, have lost their micronucleus and seem to be able to live indefinitely without a micronucleus, however, they can no longer undergo meiosis and sexual reproduction. TEM taken on 4/8/65 by R. Allen with RCA EMU3F operating at 50kV. Neg. 9,100X. raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis.
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/).
DOI: 10.6075/j00p0zg6
title: CIL: 51820, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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: 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.
DOI: 10.60719/aphrc-2025-046
title: GENOMIC AND ENVIRONMENTAL RISK FACTORS FOR CARDIOMETABOLIC DISEASE IN AFRICANS (KENYA) 2014, African Wits-INDEPTH Partnership for genetic studies on the role of the genome and environment in body composition, as a risk factor for cardiometabolic disease 2

description: The Genomic and environmental risk factor for cardiometabolic disease in Africans (AWI-Gen) project is a collaborative study between the University of the Witwatersrand (Wits) and the INDEPTH Network funded under the Human Heredity and Health in Africa (H3Africa) initiative. The H3Africa is a ground-breaking initiative to build institutional and individual capacity to undertake genetic and genomic studies in the African region. This collaboration, involves five INDEPTH sites i.e. 1) Navrongo - Ghana; 2) Nanoro - Burkina Faso; 3&4) Agincourt and Digkale - South Africa; and 5) Nairobi - Kenya) plus the Soweto-based birth-to-twenty cohort. The work in Kenya will be undertaken in the Nairobi Urban Health and Demographic Surveillance Site (NUHDSS) run by APHRC. The AWI-Gen project aims to understand the interplay between genetic, epigenetic and environmental risk factors for obesity and related cardiometabolic diseases (CMD) in sub-Saharan Africa. The project capitalizes on the unique strengths of existing longitudinal cohorts and well-established health and demographic surveillance systems (HDSS) run by the partner institutions. The six study sites represent geographic and social variability of African populations which are also at different stages of the demographic and epidemiological transitions. The study has two components: i) to understand the African population genetic structure and ii) to determine the association between genetic factors and obesity in determining cardiometabolic risk and the effect of environmental factors on this relationship.

In this application, we seek ethical approval for the Kenya study only. The other partners will seek approval from the appropriate ethics review authorities in their countries.
DOI: 10.6075/j0q23zt4
title: CIL: 53048, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 3, z=15 from SC_028
description: One z layer of a z-stack at the given image
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/j02f7mk8
title: CIL:13130, 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of quick-freeze deep-etch view of a radial arm showing a collecting canal surrounded with smooth spongiome as well as a few decorated tubules. However several larger vesicles lie next to the radial arm containing a lumen resembling the contractile vacuole. These vesicles appear to be rounded decorated tubules which have been transformed into vesicles or have not yet tubulated and become part of the decorated spongiome of the mature radial canal. Although we cannot be certain without further study we believe this may represent a dividing cell as we do know that the radial arms of the dividing cell, both their smooth and decorated spongiomes, shorten as the new CVCs develop (Allen et al., J. Cell Sci. 96:469-475, 1990; Fok et al., J. Eukaryot. Microbiol. 49:185-196, 2002. The P-face of these vesicles has a large number of IMPs like that seen in collecting canals. The highly porous E-face of several vesicles indicates that these vesicles are indeed products of the decorated spongiome. TEM taken on 6/22/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 9,780X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0cj8c56
title: CIL:17443, 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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: An early endosome in planar view that contains HRP-reaction product. This cell was exposed to HRP for 6 min. and then fixed. This early endosome had two small coated evaginations arising from its rim and also had two large HRP-containing uncoated vesicles docked next to it presumably ready to fuse with it (for this picture and a serial section showing these two vesicles and the second evagination see Fig. 14C in Allen, Schroeder and Fok, J. Cell Sci. 101:449-461, 1992). Mitochondria have an endogenous peroxidase activity. This image was adapted with permission from Fig. 14. TEM taken on 10/20/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.25µm. 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:12617) 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/).