cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.q5ed5e
title: Occurrence Download

description: A dataset containing 5722 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus mongolica",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "EventDate is greater than or equal to 1991-01-01",
 "EventDate is less than or equal to 2025-10-31"
 ]
}

 The dataset includes 5722 records from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009308-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0ns0t23
title: CIL:16227, Prochloron. In Cell Image Library

description: Freeze-fracture replica of the unicellular photosynthetic prokaryote Prochloron showing the distribution and size of particles on cleaved thylakoid membranes. 
This image group includes many other freeze-fracture images of Prochloron.

See also: Giddings TH, Withers NW, Staehelin LA.1980 Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of Prochloron sp., a prokaryote. Proc Natl Acad Sci U S A. 77:352-3566.
description: Prochloron was collected at Coconut Island, Oahu, Hawaii. Green colonies of didemnid ascidians, Diplosoma virens, were collected from shallow waters. Green spherical cells, identified as Prochloron, were released from the ascidians by gently pressing on the colonies while flushing the surface with sea water. Cells were centrifuged, then rinsed in filtered sea water fixed with glutaraldehyde, infiltrated with glycerol and vitrified. Samples were fractured and replicated using a Balzers BA 360 freeze-etch device and examined and in a JEOL 100C TEM at 50,000X magnification. Images were recorded on film and digitized.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0b56hhg
title: CIL:26564, Mus musculus, embryonic stem cell. In Cell Image Library

description: Image shows an immuno-FISH z-series of a mouse ES cell carrying a multi-copy insertion of alpha-globin BAC showing partial co-localization of lac operator FISH signal (green) with H3K9me3 immunostaining (red). DAPI staining is blue.
description: Formaldehyde fixed cells were imaged using an IMT-2 Olympus fluorescence microscope with 60x 1.4 NA objective lens. Z-series were recorded, and the slices processed by iterative constrained deconvolution. 
See also: P Sinclair et al. 2010 Dynamic plasticity of large scale chromatin structure revealed by self-assembly of engineered chromosome regions. J Cell Biol 109:761-776.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; differences in adsorption or binding of stain
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j00g3hsx
title: CIL:34914. In Cell Image Library

description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
DOI: 10.6075/j02z146f
title: CIL:37912, Homo sapiens, epithelial cell. In Cell Image Library

description: Cultured HBE monolayers were treated with 10 µM JTE-013 for 10 min. To induce apoptosis, monolayers were exposed to 1,200 µJ/cm2 UV254 irradiation in a UV series II (Spectroline) and incubated for 2 h before fixation. Cells were fixed with 4% formaldehyde in PBS, permeabilized with 0.5% Triton, blocked and incubated with primary antibody for 1 h (50 µg/ml anti-S1P mAb (LPath Inc.)). Secondary antibody was Alexa Fluor 488 goat anti–mouse IgG. Actin was detected with Alexa Fluor 568–phalloidin (Invitrogen). DNA was detected with 5 µM DRAQ5 (Axxora). Confocal micrographs were obtained using a microscope (TCS SP5; Leica) with a 63x oil lens with an electron-multiplied cooled CCD camera 1,000 x 1,000, 8 x 8 mm2 driven by the IQ software (Andor Technologies). ImageJ was used to stack confocal sections into Z series that were then color combined and reconstructed into 3D image using MetaMorph (GE Healthcare). All images were processed further using ImageJ, Photoshop (Adobe), Illustrator (Adobe), and Quicktime Pro (Quicktime) software. This Z-series corresponds to Fig 4E from J Cell Biol. 2011. 193(4): 667-676
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; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; phalloidin; DRAQ5
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Apoptotic cells produce and transmit the bioactive lipid sphingosine-1-phosphate (S1P) during extrusion. In this confocal Z-series, an antagonist to the S1P receptor, S1P2, was used to plock signaling. High levels of S1P accumulate in the dying, unextruded cells but not in surrounding cells. The nucleus is in blue, the actin-myosin ring at the basolateral surface is in red and S1P is in green.
DOI: 10.6075/j0xd10h2
title: CIL:38986, Gallus gallus, sensory neuron. In Cell Image Library

description: Fluorescence image of bodies and axons of the mesencephalic trigeminal nucleus in a 4 day old chick embryo. The trigeminal nucleus is made up of scattered neurons along the midline of the optic tectum. This micrograph shows the optic tectum from the back. The axons are labelled on one side only. Mesencephalic trigeminal neurons are unusual in that they are primary sensory neurons (probably derived from neural crest) that develop within the central nervous system.
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 a specific protein
Visualization methods: intracellular filling
Processing history: unprocessed raw data
description: B0001660 Cell bodies and axons. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0sq8z0f
title: CIL:37315, Cavia porcellus, pancreatic acinar cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification x2,000.
description: Scanning electron micrograph of single guinea pig pancreatic acinar cell. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j05q4vdg
title: CIL:1073, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 2 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: 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: 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/j0zk5g88
title: CIL: 53045, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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
description: Image 3, z=12 from SC_028
DOI: 10.6075/j0tx3fg0
title: CIL:35809, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged MCM1. 
 
 MCM1 is a transcription factor involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes
 
These phase,gfp images are part of an image group that ranges from CIL:35880-35899. 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/j0sj1k5r
title: CIL: 52732, 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: Tile x=4, y=3, z=14 from PS11_10021_2B_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0kp829h
title: CIL:43408, Mus musculus, mammary adenocarcinoma. In Cell Image Library

description: Wound Healing Assay
Time series DIC images of mouse DA3 cells, derived from the mouse mammary adenocarcinoma cell line D1-DMBA-3, induced in BALB/C mice by dimethylbenzanthracene were grown to 90% confluence. A scratch approximately 300um wide was made in the cell monolayer, and images were recorded every 14.5 min for 26 hr.
This time series image, obtained with no HGF/SF treatment, is part of a group of 17 time series images (CIL:43401 to CIL:43417) representing three different treatments: (1) no HGF/SF (CIL:43406 to CIL:43411), (2) with HGF/SF (CIL:43401 to CIL:43405), activating HGF/SF-Met signaling, and (3) with PHA (Met inhibitor) and HGF/SF (CIL:43412 to CIL:43417). The group also includes two movies (CIL:43418 and CIL:43419) created from the time series CIL:43402 and CIL:43406 respectively.
description: DA3 cells expressing the fluorescent protein mCherry were grown to 90% confluence in wells of 2 cm diameter in DMEM supplemented with 10% heat-inactivated FCS (Gibco-BRL) and treated with or without the Met inhibitor PHA665752 (2.5 µM) for 2 hrs. A scratch was generated using a 200 µl tip, and the cells were incubated with or without 80 ng ml-1 Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and subjected to time lapse confocal laser scanning microscopy (CLSM-510, Zeiss, Germany) for approximately 26 hrs, with images taken at 14.5 min intervals. The position of each scratch was predefined, and a macro that repetitively positions the microscope on each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence (shown here) was used for the multi-cellular analysis; the red fluorescence channel was exploited for single cell tracking.
See also: Zaritsky A, Natan S, Ben-Jacob E, Tsarfaty I (2012). Emergence of HGF/SF -induced Coordinated Cellular Motility. PLOS ONE 7(9): e44671
description: Preparation: living tissue
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
DOI: 10.6075/j0fx78wd
title: CIL: 50895, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Heat shocked Saccharomyces cerevisiae cells (38 oC for up to 90 minutes) were high pressure frozen and embedded in HM20 resin. Samples were then stained for Ubiquitin with the polyclonal antibody ab19247 (Abcam) and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events. The black gold particles represent the presence of Ubiquitin.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Heat shocked cells were cultured in YPD medium and high pressure frozen in a Wohlwend Compact 3 machine,
 followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. For the immuno-EM, samples were blocked for 2 hours in 0.8% BSA with 0.1% fish skin gelatine. A 1:10 dilution of the primary antibody ab19247 (Abcam) was used and a 1:20 dilution of the secondary antibody anti-Rabbit IgG 10 nm gold (Cat#25108, Electron microscopy sciences). Finally, samples were post fixed in 2.5% glutaraldehyde for 20 minutes. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead 
citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
DOI: 10.6075/j0gq6wgb
title: CIL:12292, Mus musculus, epithelial cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Cy2; X-Rhodamine; Cy5
Data qualification: Raw;spatialmeasurements
description: Colocalization of the microtubule anchoring factor LL5α (red) with integrin α6 (blue) in the basal cortex of outer epithelium of mouse mammary gland tissue, and laminin (green) in the basement membrane. Overall findings from this publication showed that signaling from laminin-integrin associations play a role in attaching microtubule plus ends to the epithelial basal cell cortex. This image is the original data file from Fig. 4Bb, J Cell Biol (2010) 189 (5):901-917.
description: Mammary tissues from C57BL6/J strain mice (8 wk of age) were prepared by perfusion fixation, processed as described previously (Nakatani et al., 2004), and immunostained for laminin (Cy2, 488 nm laser), LL5 (rhodamine red-X, 543 nm laser) and integrin a6 (Cy5, 633 nm laser), and observed using a confocal laser-scanning microscope system.
DOI: 10.6075/j0r49qs2
title: CIL:36167, Rattus, multipolar neuron. In Cell Image Library

description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density of presynaptic contacts along the dendritic arbor.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0dj5fm1
title: CIL:32059, Homo sapiens, osteocarcenoma. In Cell Image Library

description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0cn7415
title: CIL:36366, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Male Sprague Dawley rats, 4 weeks of age, were anesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy, cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. Lucifer Yellow. The astrocytes were filled using 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60x oil objective (NA 1.4). Additional details are provided in 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.
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of a 4 week old rat reveals highly ramified spongiform processes. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled here as a single maximum projection image. 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
Visualization methods: lucifer yellow
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j06t0kff
title: CIL:38815, Clostridium difficile. In Cell Image Library

description: B0006630 2007 Collection: Medical Photographic Library Copyrighted work available under Creative Commons by-nc-nd 2.0 UK: England & Wales, see http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Preparation: dispersed cells in vitro
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions
Processing history: color-enhanced
description: A colour-enhanced scanning electron micrograph image showing a cluster of Clostridium difficile on a surface. Clostridium difficile is a species of Gram-positive bacteria that causes severe diarrhea and other intestinal disease when competing bacteria in the gut flora have been wiped out by antibiotics.