cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0sf2tth
title: CIL:13464, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the pik1-83 mutant strain at permissive temperature of 26C. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4D 26C pik1-83 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
DOI: 10.6075/j09k48zg
title: CIL:13477, Drosophila melanogaster, garland cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: fluorescence microscopy; confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of a specific nucleic acid sequence; distribution of epitope
Visualization methods: EGFP; Cy5; Cy3; Deep-red fluorescent Nissl stain
Data qualification: Raw
description: Ema localizes to endosomes. Third instar larval garland cells expressing Ema-GFP fusion protein and stained for the late endosomal and lysosomal protein Spinster (red) and plasma membrane and nuclei (blue). Ema co-localizes with some late endosomes. Wandering third instar larvae were dissected in ice-cold PBS, equilibrated in HL-3 buffer at room temperature, incubated in 0.7% HRP for 5 min at room temperature, rinsed thoroughly and fixed with Bouin's solution for 5 min. Blocking and antibody incubation were performed in PBS containing 0.1% Triton X-100. Anti-Spinster antibody (Sweeney and Davis, 2002) used at 1:250. NeuroTrace 640/660 deep red fluorescent Nissl (Invitrogen) used at 1:500 was used to stain nuclei. Cy5-conjugated anti-HRP (Jackson Immunoresearch Laboratories) at 1:1000 was used to stain plasma membrane. Cy3-conjugated secondary antibody (Jackson Immunoresearch Laboratories, Inc.) at 1:1,000. Confocal images were acquired with a confocal microscope (model C1; Nikon) and accompanying EZ-C1 software using argon (excitation at 488 nm) and HeNe (excitation at 543 and 633 nm) lasers and a 60x Plan-Apochromat NA 1.4 objective (Nikon) at room temperature. Samples for each experiment were processed using the same confocal gain setting. Image corresponds to Fig 3B in Kim et al. J Cell Biol. 188: 717-734. 2010.
DOI: 10.6075/j0vq31dc
title: CIL:13479, Drosophila melanogaster, garland cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: fluorescence microscopy; confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; Cy3
Data qualification: Raw
description: Ema localizes to endosomes. Third instar larval garland cells expressing Ema-GFP fusion protein and stained for the multivesicular body ESCRT protein Hrs (red). Ema does not localize to MVB. Wandering third instar larvae were dissected in ice-cold PBS, and fixed with Bouin's solution for 5 min. Blocking and antibody incubation were performed in PBS containing 0.1% Triton X-100. Anti-HRS-FL (Lloyd et al., 2002) was used at 1:1,000. Cy3-conjugated secondary antibody (Jackson Immunoresearch Laboratories, Inc.) at 1:1,000. Confocal images were acquired with a confocal microscope (model C1; Nikon) and accompanying EZ-C1 software using argon (excitation at 488 nm) and HeNe (excitation at 543 and 633 nm) lasers and a 60x Plan-Apochromat NA 1.4 objective (Nikon) at room temperature. Samples for each experiment were processed using the same confocal gain setting. Image corresponds to Fig 3D in Kim et al. J Cell Biol. 188: 717-734. 2010.
DOI: 10.6075/j0qc0285
title: CIL:13473, Drosophila melanogaster, garland cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: uranyl salt; lead salt; osmium tetroxide; horseradish peroxidase
Data qualification: Raw;intensitiesquantitation
description: Transmission electron micrograph of Drosophila nephrocyte garland cell from ema[1] mutant pulsed with the fluid-phase endocytic tracer HRP, detected by chromogenic staining (DAB). HRP reaction product in most labeled endosome from ema[1] mutant cells does not fill the luminal space as in wild type, but instead is concentrated along the limiting membrane and in intraluminal clusters, which often extend from the limiting membrane. Third instar larvae were dissected in ice-cold PBS, equilibrated in HL-3 buffer at room temperature, incubated in 0.7% HRP (Sigma-Aldrich grade VI) for 5 min at room temperature, rinsed thoroughly, and chased for 10 min at room temperature. Samples were fixed for 1 h at 4°C in 2% paraformaldehyde, 2% glutaraldehyde, and 1% tannic acid in 0.1 M cacodylic acid buffer, pH 7.2, and processed for DAB reaction as described previously (Kosaka and Ikeda, 1983). Garland cells were dissected out and fixed for 1 h at 4°C in 2% paraformaldehyde, 2% glutaraldehyde, and 1% tannic acid in 0.1 M cacodylic acid buffer, pH 7.2. Then, the samples were postfixed in 1% OsO4 in 0.1 M cacodylic acid buffer, pH 7.2, for 1 h at room temperature, stained en bloc with 1% uranyl acetate, dehydrated in a grade series of ethanol and propylene oxide, and embedded in epon resin (Electron Microscopy Sciences). Blocks were sectioned in an ultramicrotome (RMC Products) at ∼70-nm thickness with a Delaware Diamond knife and post-stained for 1 h in Reynolds lead citrate and uranyl acetate. Electron micrographs were taken on a transmission electron microscope (H-7500; Hitachi) using an AMT camera system. Mag: 40000x. Image corresponds to Figure 4C, bottom panel in Kim et al. J Cell Biol. 188: 717-734. 2010.
DOI: 10.6075/j0jw8ckk
title: CIL:13469, Drosophila melanogaster, garland cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; charge coupled device (CCD)
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; osmium tetroxide
Data qualification: Raw;intensitiesquantitation
description: Transmission electron micrograph of Drosophila nephrocyte garland cell from ema[1] mutant: high magnification view. ema mutant garland cells are filled with very large electron-lucent alpha and electron-dense beta vacuoles, many of which are 5–10 microns in diameter, whereas the largest vacuoles in wild type are ∼2 microns in diameter. In wild type, both types of vacuoles usually contain a single aggregate of electron-dense granular material that appears to be attached to the limiting membrane. However, the large vacuolar compartments in the mutant contain numerous electron-dense granular structures, suggesting they arise from homo-/heterotypic fusions of alpha and beta vacuoles. Samples for TEM were fixed for 1 h at 4°C in 2% paraformaldehyde, 2% glutaraldehyde, and 1% tannic acid in 0.1 M cacodylic acid buffer, pH 7.2. Then, the samples were postfixed in 1% OsO4 in 0.1 M cacodylic acid buffer, pH 7.2, for 1 h at room temperature, stained en bloc with 1% uranyl acetate, dehydrated in a grade series of ethanol and propylene oxide, and embedded in epon resin (Electron Microscopy Sciences). Blocks were sectioned in an ultramicrotome (RMC Products) at ∼70-nm thickness with a Delaware Diamond knife and post-stained for 1 h in Reynolds lead citrate and uranyl acetate. Electron micrographs were taken on a transmission electron microscope (H-7500; Hitachi) using an AMT camera system. Mag: 15000x. Image corresponds to Figure 2C, right ema[1] panel in Kim et al. J Cell Biol. 188: 717-734. 2010. This is a high magnification from same region as micrograph CIL# 13468.
DOI: 10.6075/j0x63km4
title: CIL:13386, Homo sapiens. In Cell Image Library

description: This image is part of a group of 4 images supporting the conclusion that hRio2 kinase activity is required for cytoplasmic 18S-E pre-rRNA processing. This image is a control for the experiment and shows the distribution of all 18S rRNA precursors (white), via fluorescence in situ hybridization (FISH) with a 5' ITS1 probe, upon depletion of a protein important in rRNA processing, hRio2,in Hela cells. Depletion of hRio2 leads to the accumulation of 18S-E pre-rRNA in the cytoplasm (white). For the set of four images in this group, FISH pictures were processed in parallel by enhancing levels, followed by setting gamma correction to 0.75.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: microscopy
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific nucleic acid sequence
Visualization methods: Cy5
Data qualification: Processed
DOI: 10.15468/dl.28yus9
title: Occurrence Download

description: A dataset containing 3545 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chaenomeles speciosa"
 ]
}

 The dataset includes 3545 records from 291 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009600-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0m61jdg
title: CIL:12995, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution image of a part of the CVC complex with some filled ampullae present. Masses of collapsed CV membrane are associated with the 11 microtubular ribbons. Ribbon 9 is curving away from the other ribbons and is extending out over an ampulla where it will continue along the full length of this radial arm. TEM taken on 3/27/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,250X. This digitized image is 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
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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.5517/ccdc.csd.cc2m6z72
title: CCDC 2419774: Experimental Crystal Structure Determination

description: Related Article: Xiaojiao Yang, Xiao-Lin Ye, Shu-Han Bao, Dong-Nan Yu, Wenya Jiang, Bintao Wu, Shuaiqi Wang, Kangzhou Wang, Tang Yang, Guozong Yue, Samia Kahlal, Jean-Yves Saillard, Jean-François Halet, Jianyu Wei, Kuan-Guan Liu|2025|Aggregate|6|e70092|doi:10.1002/agt2.70092
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: 10.6075/j0222t0f
title: CIL:1308, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the b-tubulin immunogold labeled microtubules that arise from the apex of the cytoproct ridge and pass to the spent DV membrane. Trichocyst and trichocyst tip included in this image. TEM taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. 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
DOI: 10.5517/ccdc.csd.cc2m6z83
title: CCDC 2419775: Experimental Crystal Structure Determination

description: Related Article: Xiaojiao Yang, Xiao-Lin Ye, Shu-Han Bao, Dong-Nan Yu, Wenya Jiang, Bintao Wu, Shuaiqi Wang, Kangzhou Wang, Tang Yang, Guozong Yue, Samia Kahlal, Jean-Yves Saillard, Jean-François Halet, Jianyu Wei, Kuan-Guan Liu|2025|Aggregate|6|e70092|doi:10.1002/agt2.70092
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/ccdc.csd.cc2m6z94
title: CCDC 2419776: Experimental Crystal Structure Determination

description: Related Article: Xiaojiao Yang, Xiao-Lin Ye, Shu-Han Bao, Dong-Nan Yu, Wenya Jiang, Bintao Wu, Shuaiqi Wang, Kangzhou Wang, Tang Yang, Guozong Yue, Samia Kahlal, Jean-Yves Saillard, Jean-François Halet, Jianyu Wei, Kuan-Guan Liu|2025|Aggregate|6|e70092|doi:10.1002/agt2.70092
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: 10.6075/j07m077v
title: CIL:130, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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/).
description: The contractile vacuole pore is coated on its cytosolic side by helically wound microtubules. Other microtubules abut this helix and extend out to the surface of the contractile vacuole where they are attached to the CV membrane and hold the contractile vacuole in place. The plasma membrane and CV membrane are separated only by a narrow gap at the bottom of the pore. TEM taken on 2/11/71 by R. Allen with Hitachi HU11A operating at 60kV. Neg. 19,500X. Bar = 0.2µm. There is a high resolution version of this image in the library (CIL:39793) 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
DOI: 10.5517/ccdc.csd.cc2m6zb5
title: CCDC 2419777: Experimental Crystal Structure Determination

description: Related Article: Xiaojiao Yang, Xiao-Lin Ye, Shu-Han Bao, Dong-Nan Yu, Wenya Jiang, Bintao Wu, Shuaiqi Wang, Kangzhou Wang, Tang Yang, Guozong Yue, Samia Kahlal, Jean-Yves Saillard, Jean-François Halet, Jianyu Wei, Kuan-Guan Liu|2025|Aggregate|6|e70092|doi:10.1002/agt2.70092
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/ccdc.csd.cc2m9ymj
title: CCDC 2422638: Experimental Crystal Structure Determination

description: Related Article: Hamideh Shirazi, Kaveh Imani, Behrouz Notash, Ayoob Bazgir|2025|J.Org.Chem.|||doi:10.1021/acs.joc.5c00728
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: 10.6075/j0rn374n
title: CIL:1299, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 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.
DOI: 10.5517/ccdc.csd.cc2m9ynk
title: CCDC 2422639: Experimental Crystal Structure Determination

description: Related Article: Hamideh Shirazi, Kaveh Imani, Behrouz Notash, Ayoob Bazgir|2025|J.Org.Chem.|||doi:10.1021/acs.joc.5c00728
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: 10.6075/j04f1q07
title: CIL:1298, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 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.
DOI: 10.5517/ccdc.csd.cc2mdpf5
title: CCDC 2425267: Experimental Crystal Structure Determination

description: Related Article: Peiqing Cai, Xuhui Feng, Jing Wang, Shala Bi, Zhaoyang Chen, Xiangfu Wang, Zugang Liu|2025|Laser Photonics Rev.|||doi:10.1002/lpor.202501665
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/ccdc.csd.cc2mg9t7
title: CCDC 2426829: Experimental Crystal Structure Determination

description: Related Article: Tongwei Zhang, Xiaofeng Yuan, Ze Xu, Yuangang Xu, Ming Lu|2025|Cryst.Growth Des.|||doi:10.1021/acs.cgd.5c01019
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.