cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0g73d1r
title: CIL:39321, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Quick-freeze deep-etch of granulo-fibrillar material at the crests of the ridges. This material is composed of thinner and shorter filaments that, like the striated bands, appear to bind to the membrane. The fracture plane also exposed the cell‚Äôs exterior. TEM taken on 6/4/91 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 19,800X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0zp45pk
title: CIL: 52630, 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 tile position
description: Tile x=1, y=7, z=17 from PS09_287383C_Myc_Terc
DOI: 10.6075/j0513z93
title: CIL:40019, Caulobacter crescentus CB15. In Cell Image Library

description: A 512 by 512 image from the slice by slice reconstruction of a caulobacter crescentus specimen. 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: osmium tetroxide fixed tissue; cryofixed 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
Visualization methods: uranyl salt
Processing history: recorded image
Data qualification: Processed
description: Caulobacter cultures (strain 3724) were prefixed with 1% acrolein and 2.5% glutaradehyde, followed by high pressure freezing, and freeze substitution using a cocktail of 2% Osmium tetroxide, 0.5% uranyl acetate, and embedding in Durcupan. Film images were acquired using a JEOL 4000, at a magnification of 30,000X, 400.0 kV.
DOI: 10.6075/j0fj2fsf
title: CIL:2741, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0t152fs
title: CIL:36014, Rattus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Figure 396 from Chapter 15 (Cytoplasmic Inclusions) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Axodendritic synapse from mammalian (rat) central nervous system. Arrow points to one region of the synapse where an active zone is apparent on the presynaptic site in this plane of section. Image by Enrico Mugnaini. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
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
Visualization methods: osmium tetroxide
Data qualification: Processed
DOI: 10.6075/j0j38r68
title: CIL:34910. In Cell Image Library

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.
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).
DOI: 10.6075/j07m07ms
title: CIL: 53987. In Cell Image Library

description: Visualization methods: confocal microscopy
description: STE 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/j0gf0swf
title: CIL:37379, damselfly, flight muscle cell. In Cell Image Library

description: Longitudinal and cross sections showing ribbon like myofibrils regularly alternating with layers of mitochondria and SR/T tubules. Dyads are located in a grove of the mitochondrial surface. Negatives aere scanned on nikon 8000 at 4000dpi/6.3 micron scan step size, then reduced in size 4X for upload, for an effective pixel size of 25 micron.
 
 Technical details:
 Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer (pH7.2). Stored at 4C for several days. Muscle dissected out. Rinsed 3Xin buffer, postfixed in 2% PsO4 in buffer, for 1.5 hrs; rinsed 3 times in water, en-block stained in saturated aqueous uranyl acetate, embedded in Spurr. Thin sections stained in uranyl acetate and lead and examined in a Philips 410 Microscope.
 
 Reference for the image:
Loesser, K.E., Castellani, L. and Franzini-Armstrong, C. Disposition of junctional feet in muscles of invertebrates. J. Muscle Research Cell Motility 13:161-173, 199
description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j02v2f6h
title: CIL:4654, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Purified rabbit skeletal muscle myosin in 0.6M KCl was adsorbed onto mica flakes, quick frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress (Heuser JE, J. Mol.Biol. 1983. 169:155-195). The sample was freeze-fractured and deep-etched in a Balzers 400 freeze fracture device, and rotary-replicated in Pt-C at 11 degrees. 

This image was recorded at 100,000x in a JEOL 100CX2 transmission electron microscope operating at 100 kev, on Kodak 4489 film. The image was digitized using a Nikon Coolscan 9000ED scanner at 20 micron pixel size.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
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
DOI: 10.6075/j0sj1kpg
title: CIL:32327, Homo sapiens, endocrine-paracrine cell of prostate gland, basal cell of prostate epithelium, luminal cell of prostate epithelium, blood vessel endothelial cell, perineural cell, sheath cell, leukocyte, prostate stromal cell, smooth muscle cell of prostate. In Cell Image Library

description: Preparation: acetone fixed tissue; tissue in polyethylene glycol embedment
Relation to intact cell: cryostat-sectioned tissue
Item type: recorded image
Imaging mode: widefield illumination; bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein; differences in intrinsic optical density
Visualization methods: hematoxylin; primary antibody plus labeled secondary antibody; horseradish peroxidase; 3,3'-diaminobenzidine (DAB); biotin-avidin amplification
Processing history: unprocessed raw data
Data qualification: Raw;intensitiesquantitation
description: CD105 Immunostain of Human Prostate. Tissue section of human prostate containing adenocarcinoma that has been immunostained for the cell-surface antigen CD105. Nuclei are stained in blue.This image is part of a collection of images generated from several specimens to characterize the distribution of CD105 in human prostate tissue. 

This image is part of a large collection of immunohistochemistry images of cell-surface antigens generated by the SCGAP Urologic Epithelial Stem Cells (UESC) Project. The overall goal of the project is to characterize and isolate epithelial stem cell populations from two urologic organs, the prostate and bladder. Links are provided below for the UESC Project database, the entire human prostate immunostain summary, the CD105 immunostain summary, and information on the specimen that this image is from. Other images of CD105 human prostate immunostains are accessible following the group link.
description: The "Image ID" for this image is provided in the Attribution section. Because the images are systematically named, information such as the antibody used in staining, the organism, tissue type, tissue block, and magnification are all encoded in the Image ID. As an example, the image 'CD44 98-395F HP ba 100.jpg' was stained with anti-CD44, was derived from human prostate tissue block 98-395F, is human prostate tissue (HP), and an image of microscopic field of view b within field a was captured at 100× magnification.


Complete technical details available in the Protocol Section of SCGAP UESC website (link provided). Briefly, radical prostatectomy specimens were transverse-sectioned 3mm thick and tissue blocks were embedded in precooled OCT (Tissue-tek) medium. Frozen tissue blocks were thin-sectioned (5µ) and fixed in cold acetone. A monoclonal primary antibody (PharMingen) was used followed by a biotinylated secondary antibody. Bound antibody was detected using avidin-biotin-peroxidase (Vector Labs) and diaminobenzidine (DAB). Sections were lightly counterstained with hematoxylin. Images were acquired using a digital camera and either an Olympus BX41 or Olympus BH2 microscope.
DOI: 10.6075/j0319twq
title: CIL:2706, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.15468/dl.hnpsgv
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Fraxinus pennsylvanica"
 ]
}

 The dataset includes 22 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009249-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0dv1jn9
title: CIL: 54575, Xenopus Laevis, Entire Organism. In Cell Image Library

description: Imaging mode: RGB
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
description: 16.4 degrees C
description: Video of African clawed frog embryonic development. Video filename format is as follows organism_temperature_batch. Data was collected at 16.4 degrees Celcius
DOI: 10.6075/j0h70dz1
title: CIL:19325, Balamuthia mandrillaris, cell by organism, eukaryotic cell, Eukaryotic Protist, Amoeboid Protist. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue; whole mounted tissue
Item type: microscopy; in-focus phase contrast
Imaging mode: retardance; phase contrast microscopy
Parameter imaged: boundaries between regions with different refractive index
Source of contrast: boundaries between regions with different refractive index
Visualization methods: natural boundaries
Processing history: living tissue; recorded image; charge coupled device (CCD)
Data qualification: Raw
description: Balamuthia mandrillaris was isolated from a sample of soil from a plant in the home of a child who died of amebic encephalitis. 

These free living amoebae can be opportunistic pathogens, and in some cases have been diagnosed as the causative agent of the usually fatal amebic encephalitis. Balamuthia feed by inserting the tips of their pseudopodia into cells. Naegleria and Acanthamoeba, other opportunistic amoeboid pathogens, feed by phagocytosis. 

The cells were grown in axenic media. Then they were photographed with a Canon Power Shot G3 with a setting at ISO 50 with an optical microlens at 4X and the quality set at RAW. The camera was attached to the phototube of the microscope with a 3X lens and photographed in phase contrast with a 100X oil immersion objective. Live amoebae were placed in a chamber prepared by inverting a coverslip with/or without cultured mammalian cells onto a 3X1 inch microscope slide with a thin rim of Vaseline; melted paraffin was brushed around the edge of the coverslip to seal it to the slide. Such cultures could be maintained for several days at room temperature. Further details are available in the attached publication. Other members of the linked video group are Naegleria and Acanthamoeba.
DOI: 10.6075/j09s1qsj
title: CIL: 54595, Mus musculus, Fetal Liver Macrophage. In Cell Image Library

description: LY294002 treated
description: Processed data
description: Imaging mode: Lattice Light Sheet Microscope
Visualization methods: ChimeraX
DOI: 10.6075/j05h7gcj
title: CIL:36345, Rattus norvegicus, astrocyte. In Cell Image Library

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: Alexa Fluor 488; Alexa Fluor 568
Data qualification: Processed
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 4 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Alexa 488 (green) and Alexa 568 (red). Optical sections were generated with a single photon confocal microscope and compiled to produce this maximum projection image.
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 4 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Alexa 488 (green) and Alexa 568 (red). Optical sections were generated with a single photon confocal microscope and compiled to produce this 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.
DOI: 10.15468/dl.8kmvqs
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Epilobium amurense"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009250-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0h70fwj
title: CIL:39654, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
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
DOI: 10.6075/j07081j7
title: CIL:36439, Rattus norvegicus, astrocyte of the hippocampus, astrocyte. In Cell Image Library

description: Male Sprague Dawley rats 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 either 5% aq. lucifer yellow. The astrocytes were filled using a 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, and subsequently immunostained. 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) 60× oil objective (NA 1.4). Optical z resolution is 0.25µm. 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 a 1-week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow (green) and immunostained to reveal the localization of glial-specific proteins S-100 (red) and GFAP (blue). Optical sections were generated with a single photon confocal microscope. 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; Alexa Fluor 568; X-Rhodamine; primary antibody plus labeled secondary antibody
Data qualification: Processed