cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0g44p8j
title: CIL:36269, Vorticella convallaria, 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: 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: Cytopharynx with numerous folded membrane ribs subtended by five or so microtubules. These microtubules have arms that bind to other microtubules and to the membrane of the cytopharynx and to surrounding vesicles of various sizes. The vesicles are uncoated and free of ribosomes. The vesicles are probably equivalent to the discoidal vesicles and/or to the 100nm vesicles; the latter arise from the endosomal pathway of Paramecium. Evidence for vesicle fusion to the cytopharynx membrane, between the ribs, can be seen. Bacteria and tips of cilia are present in the lumen of the cytopharynx. TEM taken on 4/6/72 by R. Allen with Hitachi HU11A operating at 75kV. Mag. 19,500X. 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:39460) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0cf9nvt
title: CIL:13571, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Wild-type Arf1-GFP (Arf1(WT)-GFP) (gray) colocalizes primarily at the Golgi (Giantin) (red) with Helix Pomatia Lectin (HPL) (green) in unstimulated HeLa cells. HPL binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL indicates distribution of GalNac-Ts. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa 594 for anti-Giantin. Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic, UPLSAPO; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 7A, left 2 panels in J Cell Biol. 189: 843-858. 2010. Images in Fig 7 include CIL#s 13571, 13572, 13573, 13574, 13575, 13576, 13577.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; EGFP; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0w957w2
title: CIL:13567, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: GalNac-T1 staining (green) colocalizes with COP-I beta1 (red) staining at the Golgi (HPL) (gray) in unstimulated HeLa cells. Helix Pomatia Lectin (HPL) binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-GalNac-T1, Alexa 594 for anti-COP-I beta1). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 6C, in J Cell Biol. 189: 843-858. 2010. Images in Fig 6 include CIL#s 13563, 13564, 13565, 13566, 13567, 13568, 13569, 13570.
DOI: 10.6075/j0st7njj
title: CIL:13599, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Mouse hind limb tibialis anterior (TA) muscles were injected with BaCl2 followed by daily systemic administration of rapamycin (Rap) starting 7 days after injury. The animals were sacrificed at different days, and the injured muscles were dissected and cryosectioned followed by hematoxylin (blue) and eosin (pink to red) staining.

This image shows the regeneration of muscle tissue fourteen days after the injury with daily systemic administration of Rap from day 7 to day 13 and a single dose of adenovirus expressing follistatin was injected into the injured TA muscle on day 7. The growth inhibition of myofibers by Rap was rescued by recombinant follistatin expression. Myofibers were stained by eosin in red and nuclei were stained by hematoxylin in blue. This image corresponds to Fig 10B from JCB 189: 1157-1169, 2010. See also CIL: 13595, 13596, 13597, 13598, and 13600.
description: Preparation: cryostat-sectioned tissue; Fix in liquid nitrogen–cooled 2-methylbutane
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain; compartmentalization of stain or label
Visualization methods: hematoxylin; eosin
Processing history: Brightness and Contrast Adjusted
Data qualification: Processed;spatialmeasurements
description: TA muscles were isolated by dissection, frozen in liquid nitrogen–cooled 2-methylbutane, and embedded in TBS tissue freezing medium. Sections of 10-μm thickness were made with a cryostat at -20°C, placed on uncoated slides, and stained with hematoxylin and eosin. The stained slides were examined with a microscope (DMI 4000B), and the images were captured with a Fluotar 20× 0.4 NA dry objective (Leica) using a camera (RETIGA Exi). The images were processed as 24-bit colored images using Photoshop.
DOI: 10.6075/j0n878j7
title: CIL:13570, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: GalNac-T1 (green) is in dispersed punctate structures that stain positive for COP-I gamma1 (red) after EGF treatment of HeLa cells for 4h. These data suggest that GalNAc-Ts are being redistributed from the Golgi apparatus to the ER by a process that requires COP-I vesicles. Helix Pomatia Lectin (HPL) binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HeLa cells were serum starved overnight in DME (noFBS) and then treated with human recombinant EGF (100 ng/ml; Sigma-Aldrich) for 4h. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-GalNac-T1, Alexa 594 for anti-COP-I gamma1). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 6F, in J Cell Biol. 189: 843-858. 2010. Images in Fig 6 include CIL#s 13563, 13564, 13565, 13566, 13567, 13568, 13569, 13570.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0ht2n1f
title: CIL:13569, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: GalNac-T1 staining (green) colocalizes with COP-I gamma1 (red) staining at the Golgi (HPL) (gray) in unstimulated HeLa cells. Helix Pomatia Lectin (HPL) binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-GalNac-T1, Alexa 594 for anti-COP-I gamma1). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 6E, in J Cell Biol. 189: 843-858. 2010. Images in Fig 6 include CIL#s 13563, 13564, 13565, 13566, 13567, 13568, 13569, 13570.
DOI: 10.6075/j02b8z21
title: CIL:10247, Rattus, multipolar neuron. In Cell Image Library

description: Early stages of dendritic development and synapse formation in cultured hippocampal neurons. This multilayer image shows neurons fixed at 3 days in vitro and immunostained for the dendritically localized protein MAP2 (green) and the presynaptic vesicle protein Synapsin I (red). Unstained axons in the field are evident in the phase channel, which is hidden but can be turned on in the viewer. Neurons at 3, 5 and 7 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, warmed to 37°C prior to fixation, 15 minutes), permeabilized with 0.25% Triton (7 minutes) and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 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; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.15468/dl.bgcyxe
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bauhinia viridescens"
 ]
}

 The dataset includes 46 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009428-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0kw5dsv
title: CIL:13549, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: In unstimulated HeLa cells, GalNac-T1 (gray) and Helix Pomatia Lectin (HPL) (green) colocalize exclusively at the Giantin-stained Golgi apparatus (red). The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Giantin, Alexa 594 for anti-GalNac-T1). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. The amount of GalNac-T1 (blue) staining or HPL staining (green) colocalizing with Golgi membranes (red) was compared between unstimulated and 4h EGF-treated HeLa cells using fixed laser power and detector voltages. The quantification is graphed in Fig2D. Image corresponds to Fig 2C, top panel, unstimulated, in J Cell Biol. 189: 843-858. 2010. Images in Fig 2 include CIL#s 13547, 13548, 13549, 13550.
DOI: 10.6075/j0kh0m1s
title: CIL:13552, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Helix Pomatia Lectin (HPL) (green) colocalizes at the Golgi (Giantin) (red) in unstimulated HeLa cells. The image also shows GalNac-T1 staining (gray). The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS) and treated with DMSO for 4 h. Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-Giantin, Alexa 594 for anti-GalNac-T1). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 3A, top left panel, in J Cell Biol. 189: 843-858. 2010. Images in Fig 3 include CIL#s 13551, 13552, 13553, 13554.
DOI: 10.6075/j0319tv8
title: CIL:2649, 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: 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: 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 12 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: 10.6075/j08c9v0g
title: CIL:12580, Spiroplasma kunkelii, Dalbulus maidis, prokaryotic cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized 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; distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; propidium iodide
Data qualification: Processed
description: Confocal laser scanning micrograph of immunofluorescence-labeled corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) aggregates (green) in whole mount preparations of its leafhopper vector D. maidis, showing the anterior and posterior midgut. Whole-mount organs were labeled with primary CSS antibodies then with secondary antibodies (Alexa Fluor-488, green), and stained with the nuclear stain propidium iodide (red). CIL:19118, from the same image group, is a labeled version of this. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. For additional information refer to Ammar and Hougenhout(2005)
Ann. Entomol. Soc. Am. 98(6): 820Ð826.