cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0vx0ftn
title: CIL:38688, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution of cell in mitosis. The nuclear envelope of the micronucleus becomes heavily and uniformly labeled with anti-b-tubulin which is not in the form of microtubules. Some tubulin is also present inside the micronucleus. Apparently b‚Äìtubulin is being recruited to the mitotic micronucleus to form the spindle inside the intact micronucleus. Microtubules are present in the cytosol. TEM taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 7,900X.
DOI: 10.6075/j0qr4vsq
title: CIL:37199, Cavia porcellus, pancreatic cell. In Cell Image Library

description: Transmission electron micrograph of mitochondria from guinea pig pancreas. The use of osmium tetroxide as a fixative for electron microscopy was first described by Dr. Palade at the Rockefeller. Another major advance in fixation for electron microscopy was done at Yale by David Sabatini who described the use of glutaraldehyde which not only preserved ultrastructure, but enzymatic activities which opened up the possibility of EM localization of enzymatic function in cells. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
description: References:
Palade, G.E. 1952. J. Exp. Med. 95:285-298.
Palade, G.E. 1952. Anat. Rec. 114:427-451.
Sabatini, D.D, K. Bensch and R.J. Barrnett. 1963. J. Cell. Bio. 17:19-58. 
Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification 56,000.
DOI: 10.6075/j0ww7gzg
title: CIL:832, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons; widefield illumination; wide-field detection
Parameter imaged: electron density
Source of contrast: electron density; elevation
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Purified rabbit skeletal muscle myosin in 0.6M KCl was deposited onto mica flakes, 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 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope at 100 kev.
 
 Images were recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED.
 
 Note the classic appearance of the individual molecules with two globular heads (myosin subfragment 1) and the long rod-like tail.
 
 RIGHT image of a stereo pair.
DOI: 10.6075/j02j69w7
title: CIL:7356, notopthalmus viridescens, erythrocyte. In Cell Image Library

description: Newt (Notopthalmus viridescens erythrocytes were isolated in 0.1M KCl, spread on the surface of Na-citrate, picked up on formvar-carbon films, fixed with glutaraldehyde and negatively stained with 2% uranyl acetate. 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 a stretched tangle of chromatin fibers from the dispersed nucleus.
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; uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0q52n60
title: CIL:47510, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 2)
DOI: 10.6075/j00z71wt
title: CIL:50648, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
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; 4',6-diamidino-2-phenylindole (DAPI)
description: Image was acquired with a 40x lens of an Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
DOI: 10.6075/j069738w
title: CIL: 54060, Homo sapiens, HeLa. In Cell Image Library

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.
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: Visualization methods: confocal microscopy
DOI: 10.6075/j0z89cg4
title: CIL:35903, Saccharomyces cerevisiae. In Cell Image 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 electrons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged TEM1. 
 
 TEM1 is a GTP-binding protein of the ras superfamily involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis. 
 
These phase,gfp images are part of an image group that ranges from CIL:35900-35919. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
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/j0h9957t
title: CIL:12552, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown 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
description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
Detailed methods: 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 (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
DOI: 10.6075/j0sb44dk
title: CIL:37171, Anura. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x54,000.
description: Transmission electron micrograph of desmosomes (macula adherens)in the junctional complex between cells in frog skin. The upper desmosome is cut obliquely and appears much wider than the lower (vertically located) one. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0348k6h
title: CIL: 54706, Bacteria E coli, MC1061. In Cell Image Library

description: Imaging mode: EPI on a Nikon TiE2 Hamamatsu ORCA Flash 4.0 sCMOS Camera and Nikon SR Apo TIRF 100x objective lens (NA 1.49)
description: mPAmCherry bright field with TIR-STD site, sclae bar 4 um.
description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
DOI: 10.6075/j0hd7tkf
title: CIL:35792, Saccharomyces cerevisiae. In Cell Image 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
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Read the microscopy section of the referenced paper for details prior to image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Bck2, a Cln-independent activator of CLN1,2 expression. These phase and GFP images are part of a group that ranges from CIL:35780-35799. Note that there are additional groups of images monitoring the dynamics of other proteins involved in cell cycle regulation by the same authors in the Library.
DOI: 10.6075/j0fq9vjn
title: CIL:35560, Cricetulus griseus, ovary. In Cell Image Library

description: Metaphase-arrested CHO cells were swollen in 75 mM KCL, fixed with formaldehyde, post-fixed with OsO4, embedded, and 0.25 micron sections examined by High Voltage EM. Seen is a longitudinal section through a chromatid pair with kinetochore elements. This image recorded with a specimen tilt of 75 degrees is part of a grouped tilt series ranging from 20 degrees to 75 degrees. Pairs providing oblique stereo views of chromosome organization.
description: Colcemid-arrested cells were swollen in hypotonic 75mM KCl, fixed with 4% HCOH, post-fixed with OsO4, embedded in plastic, and 'thick' 0.25 micron sections prepared. Sections were recorded using the Wisconsin HVEM at 1 MeV. See Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246; Ris (1981) Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Preparation: formaldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0gt5mcb
title: CIL:11853, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.15468/dl.6mu77v
title: Occurrence Download

description: A dataset containing 89220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((8.63275 47.30915,8.72918 47.30915,8.72918 47.38423,8.63275 47.38423,8.63275 47.30915))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is 64ee55c9-570a-42af-b7da-3f13c6b4e5a9"
 ]
}

 The dataset includes 89220 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009649-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0mw2g7p
title: CIL:11852, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j08w3cfd
title: CIL:11851, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of a chromosome at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.4121/3b9caf72-350a-4e32-97b2-2b854c1ad84a
title: Data from MSc thesis "Assessing the Impact of Tree 3D Representations on Urban Daylight Simulation Based on Airborne Laser Scanning Point Cloud Data"

description: This folder contains the 3DM files with the 3D tree representations of the study area and the analysis grid. Specifically, it includes the tree models generated using the Point Cloud–based, Voxel Grid, Alpha Shape, and Convex Hull methods for both February and June. The analysis grid was used for the daylight simulations conducted with the ClimateStudio plugin in Rhino.
DOI: 10.6075/j06t0msb
title: CIL:40090, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling; distribution of epitope
Visualization methods: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Data qualification: Processed
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 then ready to be immunolabeled. The rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
DOI: 10.4121/3b9caf72-350a-4e32-97b2-2b854c1ad84a.v1
title: Data from MSc thesis "Assessing the Impact of Tree 3D Representations on Urban Daylight Simulation Based on Airborne Laser Scanning Point Cloud Data"

description: This folder contains the 3DM files with the 3D tree representations of the study area and the analysis grid. Specifically, it includes the tree models generated using the Point Cloud–based, Voxel Grid, Alpha Shape, and Convex Hull methods for both February and June. The analysis grid was used for the daylight simulations conducted with the ClimateStudio plugin in Rhino.
DOI: 10.6075/j0gm87pw
title: CIL:57485. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-VP40 immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j0tx3frk
title: CIL:57458. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-VP40 immuno-golg labelling.
DOI: 10.6075/j03f4q1h
title: CIL:57457. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-VP40 immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section