cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03n22jp
title: CIL:12919, 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 28,500 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0154gg2
title: CIL: 51170, 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: 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.
DOI: 10.6075/j0kk99jw
title: CIL:12285, Mus musculus, fibroblast. In Cell Image Library

description: This confocal image of beta3-/- integrin cells plated on cell-derived matrices has an accompanying image of the wild type control cells. There are ncreased numbers of peripheral matrix-associated adhesions in the beta3-/- cells. The cells are co-stained for active beta1 integrin (9EG7-FITC, green), paxillin (Alexa-568, red) and fibronectin (Alexa-633, blue). Images were acquired using a Zeiss LSM 510 Meta microscope, 1024x1024 resolution, 13 stacks in the Z plane at 0.5um intervals. Images correspond to Fig 1C in J Cell Bio. 2010. 189:369-383
description: Preparation: chemically fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Fluorescein (FITC); Alexa Fluor 568; Alexa Fluor 633; primary antibody plus labeled secondary antibody
Processing history: color combine
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0s75f7d
title: CIL:25896, uncultured scuticociliate, Conchophthirus curtus, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A glancing view of the cortex of Conchophthirus reveals details of cortical structure. This includes the nature of the cell membrane and the alveolar membranes that reside immediately below the surface; fibrillar and microtubular structures that support this ciliated cell, and in the case of Conchophthirus, the cortical mitochondria that may represent a single mitochondrion that has finger-like extensions that lie immediately between the rows of basal bodies and are independent of more typical vesicular mitochondria that reside in the inner cytoplasm. The negative magnification is 19,000X. 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 65nm thickness. For greater detail see:Antipa, G. A. 1971. Structural differentiation in the somatic cortex of a ciliated protozoan, Conchophthirus curtus Engelmann, 1862. Protistologica 7:47l-501.
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
DOI: 10.6075/j02f7n59
title: CIL: 54090. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j02v2f18
title: CIL:34849, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
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: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica 100x HCX PLAN APO NA 1.35 DIC objective lens. images were captured at 5 sec intervals with a Hamamatsu ORCA-ER2 CCD camera using Simple PCI 6.6.0.0 software.
description: Movie of cell growth and division in cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) using DIC optics. This movie and the stack of time series images used to prepare them are grouped in the Cell Image Library.
DOI: 10.6075/j0q52p89
title: CIL: 53287, Homo sapiens, Anucleated structure. In Cell Image Library

description: Intra-alveolar amylacea body, concentric laminations, central undefined material
description: Hematoxilin and eosin stain.
description: Imaging mode: recorded image
Visualization methods: microscopy
DOI: 10.25442/hku.30495968
title: Supporting data for "Methane emissions in (sub)tropical aquaculture ponds: combined effects of salinity, organic matter, and temperature"

description: Aquaculture ponds are hotspots of methane (CH<sub>4</sub>) emissions. However, a mechanistic understanding of CH<sub>4</sub> production and emissions across diverse aquaculture pond types remains largely unknown. Through surveys of 20 aquaculture ponds representing diverse culture systems in (sub)tropical southern China, we examined CH<sub>4</sub> emissions (<i>F</i>CH<sub>4</sub>) and their underlying drivers. The dataset contains the physicochemical paramaters, dissolved CH<sub>4</sub> concentration and CH<sub>4</sub> emission flux of suface water in aquaculture ponds. Our study highlights the substantial CH4 fluxes in (sub)tropical aquaculture ponds and elucidates the key controls of salinity, organic matter availabity, and temperature on aquaculture pond CH4 emissions. These findings provide a framework for scaling the contribution of aquaculture ponds to the global CH4 budgets.<br>
DOI: 10.25442/hku.30495968.v1
title: Supporting data for "Methane emissions in (sub)tropical aquaculture ponds: combined effects of salinity, organic matter, and temperature"

description: Aquaculture ponds are hotspots of methane (CH<sub>4</sub>) emissions. However, a mechanistic understanding of CH<sub>4</sub> production and emissions across diverse aquaculture pond types remains largely unknown. Through surveys of 20 aquaculture ponds representing diverse culture systems in (sub)tropical southern China, we examined CH<sub>4</sub> emissions (<i>F</i>CH<sub>4</sub>) and their underlying drivers. The dataset contains the physicochemical paramaters, dissolved CH<sub>4</sub> concentration and CH<sub>4</sub> emission flux of suface water in aquaculture ponds. Our study highlights the substantial CH4 fluxes in (sub)tropical aquaculture ponds and elucidates the key controls of salinity, organic matter availabity, and temperature on aquaculture pond CH4 emissions. These findings provide a framework for scaling the contribution of aquaculture ponds to the global CH4 budgets.<br>
DOI: 10.6075/j0w37v7p
title: CIL:35533, Lilium longiflorum, gamete. In Cell Image Library

description: Preparation: unfixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: intrinsic mass distribution
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Illumination provided by a SpectraPhysics-Newport MaiTai laser with DeepSee dispersion compensation providing pulses of approximately 100 fs duration at 80 MHz. Wavelength set at 860 nm with emission at 465 to 50 nm.
Zeiss 710 multi-photon microscope with 63X N.A. 1.4 oil immersion objective. Pollen was removed from the flower, put in a coverslip bottom chamber, covered with tissue culture grade mineral oil, and imaged within 12 hours.
description: Lilium longiflorum (Easter Lily) pollen. This is a thin optical section through the center of the desiccated stage of the mature pollen showing autofluorescence or harmonic generation of intrinsic structures. The brightest signal is from the outer layer, the exine and raised pilae.
DOI: 10.6075/j0jm28d2
title: CIL:11029, Cricetulus griseus, spermatogonium. In Cell Image Library

description: This micrograph, courtesy of David Phillips, was published as Figure 134 from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the corresponding chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
description: Transmission electron micrograph of a cross section through the nucleolus from a Chinese hamster spermatogonium revealing a complex distribution of regions of varying granular textures.
DOI: 10.6075/j0gt5m29
title: CIL:35214, Mus musculus, fibroblast. In Cell Image Library

description: Time lapse movie of mouse embryonic fibroblasts in culture imaged at 30 second intervals by phase contrast microscopy. A micropipette is positioned near the cells to deliver either a growth factor or control buffer. In this sequence when a growth factor is added the cells activate a ring of ruffles that begin at the periphery and converge most likely at the site of the primary cilium followed by whole cell motility towards the pipette tip.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: These data were collected as research which led to the published article Cell Physiol Biochem 2010;25:279-292. Microscopy was performed with a 20X planapo phase contrast objective on an Olympus IX 70 microscope with a SensicamHQ cooled CCD camera and a heated stage insert set to 37 degrees C. Cells were grown and serum starved for 48 h in a coverslip bottom MatTek dish. Small amounts of PDGF-BB were continuously ejected from the micropipette to create a gradient in the vicinity of growth-arrested wt MEFs. Cell movement was monitored with time lapse video microscopy, taking images at 30 second intervals. A Femtojet Micromanipulator 5171 (Eppendorf-Brinkman Instruments) and a pump (model Femtojet; Eppendorf) were used to control the position of the micropipette and the pressure
required for the chemoattractant flow. Femptotip II micropipettes were positioned within 1 μm
of the cover slip and pressure set at 30 to 45 hPa. Spatial scale is approximate.
DOI: 10.6075/j07d2swp
title: CIL:13557, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Helix Pomatia Lectin (HPL) (gray) staining is present exclusively at the Golgi (Giantin) (green) with no significant colocalization with ER marker, PDI (protein disulfide isomerase) (red) in unstimulated HeLa cells. HPL binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Giantin, Alexa 594 for anti PDI). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 4C in J Cell Biol. 189: 843-858. 2010. Images in Fig 4 include CIL#s 13555, 13556, 13557, 13558.
DOI: 10.6075/j0057dwf
title: CIL:35130, Mus musculus, macrophage. In Cell Image Library

description: Phase contrast microscopy of living bone marrow derived macrophages. These cells are highly motile and the snapshot catches lamella and ruffles where the cells are protruding and phase dense organelles inside the volumes of the cells.
description: Cells were extracted from a mouse femur and plated in a coverslip bottom well (MatTek) in standard culture media. The Olympus IX 71 microscope had a simple heated stage. Cells were imaged with a 60X N.A. 1.4 phase 3 planapo objective with a Cooke Sensicam QE operated by IP Lab software running on a Dell Windows XP computer.

This picture is one of a series that may be composed into a montage to see a large field of cells interacting while preserving the high magnification. Some of the pixels in this and the neighboring images are saturated.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0m61jp2
title: CIL: 50766, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
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/j0bk1bd9
title: CIL:7503, gallus gallus, erythrocyte. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: spread nucleus
Item type: film
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
Visualization methods: negative staining; tungsten compound
Processing history: unprocessed raw data
description: A drop of a preparation of chicken erythrocyte nuclei was exposed to low ionic strength and centrifuged onto a formvar-carbon film, fixed with paraformaldehyde and negatively stained with sodium phosphotungstate. Images were recorded at 40KX and accelerating voltage of 1MeV at the University of Wisconsin HVEM facility.This image was taken with a specimen tilt of 55 degrees. A grouped image of the same field at a 45 degree tilt provides an oblique stereo view of the tangle of chromatin fibers in the dispersed nucleus.
DOI: 10.6075/j0zc82fm
title: CIL: 52899, 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 image
description: Image 9, z=13 from SC_007