cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0pg1qrd
title: CIL:2676, Caenorhabditis elegans. In Cell Image Library

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.
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
DOI: 10.6075/j0sj1j94
title: CIL:17444, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Micrograph following trifluoperizine (TFP) treatment, which apparently does not inhibit endocytosis but does inhibit movement of vesicles away from the parasomal sacs, coated and preendosomal vesicles and early endosomes become strongly labeled with HRP but all remain within the cortex. TFP seems to interfere with membrane movements into the cell so that even the products of coated pits arising from early endosomes, the carrier vesicles, remain in the cortex. TEM taken on 10/9/87 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Bar = 0.5µm. Adapted with permission from Fig. 15 published in J. Cell Sci. 101:449-461, 1992. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12615) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue; trifluoperizine (TFP)
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt; horseradish peroxidase
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0959g3h
title: CIL:47041, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; 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
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.
DOI: 10.6075/j0348jbw
title: CIL:36241, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Up to three basal bodies have been seen in various stages of development near a mature basal body/cilium complex. In this micrograph 2 new basal bodies are present next to 2 cilia and 3 are forming next to the third complex. Developing basal bodies can reorient parallel to the older basal body before it has elongated completely. TEM taken on 8/14/67 by R. Allen with Philips 200 operating at 60kV. Neg. 19,200X. Bar = 0.2µm. 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:39797) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; 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. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0ms3s2h
title: CIL:39772, Mus musculus, cardiac muscle cell. In Cell Image Library

description: Transmission electron micrograph showing an over view of muscle tissue configuration from a mouse cardiac muscle ventricle. This image shows muscle to muscle connection and the abundance of mitochondria illustrate their importance to heart muscle function.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment; ethanol dehydration
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: uranyl salt; lead salt
Processing history: unprocessed raw data
description: Primary fixation included: 2.5 % glutaraldehyde, 2% formaldehyde in 0.1 M Na-phosphate buffer, pH 7.4. Post-fixed in 2% OSO4 in 0.1 M Na-phosphate buffer, pH 7.4. Stained en bloc in 1% uranyl acetate. The tissue was then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph image was taken using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80kV.
DOI: 10.6075/j0k64hmk
title: CIL: 52484, 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=5, y=1, z=18 from BL32077_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j03t9h99
title: CIL:10205, Rattus, multipolar neuron. In Cell Image Library

description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 1 day in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field. Neurons at 1, 3 and 5 days in vitro are represented in this image group.

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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500, suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
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; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0gh9hgv
title: CIL: 52270, 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: Tile x=2, y=5, z=14 from BL_024216_Myc_Terc
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
DOI: 10.15468/dl.ku5zdw
title: Occurrence Download

description: A dataset containing 3296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juglans mandshurica",
 "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 3296 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009278-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j01n80nv
title: CIL: 52209, Homo sapiens. In Cell Image Library

description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
DOI: 10.6075/j0416vtd
title: CIL:12615, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution micrograph following trifluoperizine (TFP) treatment, which apparently does not inhibit endocytosis but does inhibit movement of vesicles away from the parasomal sacs, coated and preendosomal vesicles and early endosomes become strongly labeled with HRP but all remain within the cortex. TFP seems to interfere with membrane movements into the cell so that even the products of coated pits arising from early endosomes, the carrier vesicles, remain in the cortex. TEM taken on 10/9/87 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Adapted with permission from Fig. 15 published in J. Cell Sci. 101:449-461, 1992. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue; trifluoperizine (TFP)
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt; horseradish peroxidase
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.5517/cc3d18s
title: CCDC 100944: Experimental Crystal Structure Determination

description: Related Article: A.Trosch, H.Vahrenkamp|1998|Eur.J.Inorg.Chem.|1998|827|doi:10.1002/(SICI)1099-0682(199806)1998:6<827::AID-EJIC827>3.0.CO;2-Q
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3dl24
title: CCDC 101465: Experimental Crystal Structure Determination

description: Related Article: S.Sawusch, U.Schilde, A.Lehmann, E.Uhlemann|1998|Inorg.Chim.Acta|277|219|doi:10.1016/S0020-1693(97)06154-9
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3xlq9
title: CCDC 116861: Experimental Crystal Structure Determination

description: Related Article: A.Trosch, H.Vahrenkamp|1998|Eur.J.Inorg.Chem.|1998|827|doi:10.1002/(SICI)1099-0682(199806)1998:6<827::AID-EJIC827>3.0.CO;2-Q
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3xlrb
title: CCDC 116862: Experimental Crystal Structure Determination

description: Related Article: A.Trosch, H.Vahrenkamp|1998|Eur.J.Inorg.Chem.|1998|827|doi:10.1002/(SICI)1099-0682(199806)1998:6<827::AID-EJIC827>3.0.CO;2-Q
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3xlsc
title: CCDC 116863: Experimental Crystal Structure Determination

description: Related Article: A.Trosch, H.Vahrenkamp|1998|Eur.J.Inorg.Chem.|1998|827|doi:10.1002/(SICI)1099-0682(199806)1998:6<827::AID-EJIC827>3.0.CO;2-Q
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3d80r
title: CCDC 101153: Experimental Crystal Structure Determination

description: Related Article: M.Bergamo, T.Beringhelli, G.D'Alfonso, P.Mercandelli, M.Moret, A.Sironi|1998|Angew.Chem.,Int.Ed.|37|2128|doi:10.1002/(SICI)1521-3773(19980817)37:15<2128::AID-ANIE2128>3.0.CO;2-7
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3dgc9
title: CCDC 101350: Experimental Crystal Structure Determination

description: Related Article: T.Gross, R.Kempe, H.Oehme|1999|Eur.J.Inorg.Chem.|1999|21|doi:10.1002/(SICI)1099-0682(199901)1999:1<21::AID-EJIC21>3.3.CO;2-V
description: Related Article: T.Gross, R.Kempe, H.Oehme|1998|Inorg.Chem.Commun.|1|128|doi:10.1016/S1387-7003(98)00033-1
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3dlnq
title: CCDC 101483: Experimental Crystal Structure Determination

description: Related Article: K.Knabel, I.Krossing, H.Noth, H.Schwenk-Kircher, M.Schmidt-Amelunxen, T.Seifert|1998|Eur.J.Inorg.Chem.|1998|1095|doi:10.1002/(SICI)1099-0682(199808)1998:8<1095::AID-EJIC1095>3.3.CO;2-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3y2gk
title: CCDC 117318: Experimental Crystal Structure Determination

description: Related Article: M.Bergamo, T.Beringhelli, G.D'Alfonso, P.Mercandelli, M.Moret, A.Sironi|1998|Angew.Chem.,Int.Ed.|37|2128|doi:10.1002/(SICI)1521-3773(19980817)37:15<2128::AID-ANIE2128>3.0.CO;2-7
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3ylvg
title: CCDC 117826: Experimental Crystal Structure Determination

description: Related Article: K.Knabel, I.Krossing, H.Noth, H.Schwenk-Kircher, M.Schmidt-Amelunxen, T.Seifert|1998|Eur.J.Inorg.Chem.|1998|1095|doi:10.1002/(SICI)1099-0682(199808)1998:8<1095::AID-EJIC1095>3.3.CO;2-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3ylwh
title: CCDC 117827: Experimental Crystal Structure Determination

description: Related Article: K.Knabel, I.Krossing, H.Noth, H.Schwenk-Kircher, M.Schmidt-Amelunxen, T.Seifert|1998|Eur.J.Inorg.Chem.|1998|1095|doi:10.1002/(SICI)1099-0682(199808)1998:8<1095::AID-EJIC1095>3.3.CO;2-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc3ylxj
title: CCDC 117828: Experimental Crystal Structure Determination

description: Related Article: K.Knabel, I.Krossing, H.Noth, H.Schwenk-Kircher, M.Schmidt-Amelunxen, T.Seifert|1998|Eur.J.Inorg.Chem.|1998|1095|doi:10.1002/(SICI)1099-0682(199808)1998:8<1095::AID-EJIC1095>3.3.CO;2-4
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.