cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j02v2fcr
title: CIL:1447, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

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

stereo pair with CIL:1446
DOI: 10.6075/j0h41q7p
title: CIL:41553, Mus musculus, lymphocytic leukemia. In Cell Image Library

description: Phase contrast image of serum arrested mouse L-1210 cells engaged in spontaneous apoptosis (programmed cell death) after nutrient depletion and acid hydrolysis. The image was taken at 40X, scanned, and then enlarged. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
description: 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: scanned; enlarged
DOI: 10.6075/j0bz64vb
title: CIL:11439, Spermophilus citellus, Leydig cell. In Cell Image Library

description: Mitochondria can show tremendous variation in size, even within a single cell. Here, a huge spherical mitochondria of about 6-7 µm in diameter is adjacent to small elongate mitochondria 0.5 µm wide in a testicular Leydig cell of the ground squirrel Citellus lateralis. This image is courtesy of Jeffrey Pudney, and appears as Figure 247 in Chapter 7 (Mitochondria) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
DOI: 10.6075/j0j67ghn
title: CIL: 52701, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=2, z=4 from PS11_10021_2B_Myc_Terc
DOI: 10.6075/j05b026z
title: CIL: 53888, 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: OTHER 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/j0fb51p6
title: CIL:13878, Saccharomyces cerevisiae. In Cell Image Library

description: During late anaphase, Tem1 (green) localized to the spindle pole body (SPB) in cdc15-2 bfa1Δ cells grown at the restrictive temperature. DAPI (blue) and DIC (hidden) are also shown. Compare to image CIL# 13879. Image is Fig S4D, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig S4 include CIL# 13877, 13876, 13879, 13878.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa tem1::TEM1-yEGFP::SpHIS5 bfa1::HIS3 cdc15-2) grown at 37C were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
DOI: 10.6075/j02r3qh6
title: CIL:10410, Arabidopsis thaliana. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: phalloidin
Data qualification: Processed
description: Polymerized actin localization in wild type (left) and mutant (right) Arabidopsis thaliana leaf trichomes during the transition to branch elongation. The "distorted group" of trichome morphology mutants were originally identified as a class of mutants that failed to maintain polarized growth following branch initiation. Subsequent analyses indicated that distorted mutants are specifically affected in actin-dependent morphogenesis and fail to organize a polarized cytoskeleton in developing branches. Genetic experiments later proved that DISTORTED genes encode subunits of the evolutionarily conserved WAVE and ARP2/3 complexes. These heteromeric complexes translate Rho family small GTPase signals into actin filament nucleation and a coordinated growth response. Detailed methods: Intact Arabidopsis shoots were fixed in 100 mM PIPES/KOH pH 6.9, 5 mM EGTA, 4 mM MgCl2 (PEM) containing 2 % formaldehyde. Actin filaments were detected with overnight incubation with 0.2 µM Alexa Fluor 488® phalloidin. Confocal images were obtains using a Biorad Radiance 2100 confocal head mounted on a Nikon E800 stand. The objective used was a 60X 1.2 NA water immersion lens. Acquisition Parameters: Still image. Maximum projections of confocal images of the actin cytoskeleton in normal (left panel) and the ARP2/3 complex subunit mutant arpc2/distorted2 (right). Trichomes are unicellular structures that arise from single protodermal cells and usually form three highly elongated branches. br=branch, base=attachment region of the cell. Magnification: bar=20 µm. For more information see these references: Hulskamp, M., Misra, S., Jurgens, G. Genetic dissection of trichome cell development in Arabidopsis, Cell 1994, 76: 555-566. Szymanski, D. Breaking the WAVE complex: the point of Arabidopsis trichomes. Curr Opin Plant Biol 2005, 8: 103-112. The maximum projection image from the left panel has appeared as part of Fig. 3 in Kotchoni et al. (2009) Plant Physio. 151: 2095-109. Copyright American Society of Plant Biologists
DOI: 10.6075/j0d50kv4
title: CIL:36599, 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39310) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: A view of cortical fibers except the observer is looking at a cross-sectioned cell as though from anterior toward the posterior end of the cell; in this view the kd sections are seen on the left side of the ridge. Striated bands always lie closer to the epiplasm than the infraciliary lattice. TEM taken on 12/30/70 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 33,750X. Bar = 0.1µm.
DOI: 10.6075/j0057g2h
title: CIL:40083, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with Alexa 568. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were 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.
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
DOI: 10.6075/j06h4h5f
title: CIL: 54531. 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/j01r6qqq
title: CIL:55772, Homo sapiens, HEK293BR. In Cell Image Library

description: Immunofluorescence staining with primary and fluorescence-tagged secondary antibody.
description: Imaging mode: Apotome Microscopy
Visualization methods: Immunofluorscence staining
description: Treatment with Baf, LiCl, and PMA.
DOI: 10.6075/j02f7m9p
title: CIL:40487, Homo sapiens, epidermoid carcinoma. In Cell Image Library

description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met:

The publication and/or presentation are solely for informational and non-commercial purposes.

The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal 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
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody 
 HPA036022 (shown in green). HPA036022 is a polyclonal Anti-REPIN1 antibody that labels the nucleus. The cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules (red).
DOI: 10.15468/dl.bywx87
title: Occurrence Download

description: A dataset listing the 50174 species recorded in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Asteraceae",
 "TypeStatus is one of (Type, Holotype)"
 ]
}

 The dataset's 50174 records were derived from 539 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009607-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j02j6bpz
title: CIL:36894, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #12 (second time-lapse set, 60 minutes) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with ~10 minute intervals and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected ~24 hours earlier with in vivo electroporation of plasmid DNA encoding eYFP. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
 
 Images were acquired a 0, 10, 20, 30, and 50 minutes. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~4 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0639pv7
title: CIL:39999, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; tissue in epoxy resin embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Visualization methods: intracellular filling
Data qualification: Processed
description: Individual cells in fixed tissue were injected with Lucifer yellow and stored in 4% paraformaldehyde at 4° C. Fluorescence was photoconverted using DAB and a confocal laser light source. After this process, tissue was washed thoroughly in PBS and processed for EM by osmication, dehydration, and embedding 
in epoxy resin. For detailed methods, see the protocol provided in the CCDB. The tomogram was generated using an Hitachi UHVEM. Single tilt images spanned -64 to 64° in 2° increments. Magnification, 3000X; accelerating voltage, 3.0 MeV.
description: Maximum intensity projection of a tomographic reconstruction of a selectively stained spiny dendrite from a striatal medium spiny neuron from the neostriatum of a wildtype mouse. This reconstructed image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database.
DOI: 10.6075/j0dr2v4n
title: CIL: 54426, Homo sapiens, astrocyte. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled for glial fibrillary acidic protein (GFAP), a protein commonly used to identify astrocytes.
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: Imaging mode: bright-field microscopy
Visualization methods: GFAP IHC using HRP/DAB
DOI: 10.15468/dl.dqye3e
title: Occurrence Download

description: A dataset containing 170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris)",
 "TaxonKey is Isoberlinia"
 ]
}

 The dataset includes 170 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009620-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0pc320d
title: CIL: 53220, Entire Organism, Overall development. In Cell Image Library

description: Video of African clawed frog embryonic development. Each video is labeled with the temperature (Celcius) at which it was captured and the name of the Time Course (##TC).
description: Imaging mode: Gray Scale
Visualization methods: Captured on a microscope using a Canon Rebel Ti5/6 or a one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
DOI: 10.6075/j0vx0fd8
title: CIL:26601, Homo sapiens, cervical epithelium. In Cell Image Library

description: HeLa cells stably expressing the BAC-encoded GFP-labeled U170K snRNP and MS2-mRED proteins and treated with doxycholine to express the E3 transgene. Shown is the mRED signal. Cells imaged witb a Leica SP5 confocal microscope using a 60x 1.4NA HCX Plan Apo objective lens. From Fig 5C in Huranova et al. 2010 J Cell Biol 191:75-86.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; pDsRED-Monomer-N1
Processing history: line averaging
Data qualification: Processed