cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0s46rp9
title: CIL: 54070, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: 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/j0tb1640
title: CIL:1630, 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 0 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/j0qv3kcp
title: CIL:44152, Mus musculus, epidermal cell, endodermal cell, muscle cell, hair follicle. In Cell Image Library

description: Imaging was performed using a Leica TCS SP5-AOBS 5-channel confocal/two-photon system equipped with multiline Argon diode 561 nm, HeNe 594 nm and HeNe 633 nm as well as TiSaph two-photon laser. Images were recorded with a 25x 0.95 NA water dipping objective lens, and 5 micrometer z-spacing and processed using Imaris software (Bitplane). 
See also: Malide D, Metais J-Y, and Dunbar CE. (2012). Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy. Blood. Dec 20;120(26):e105-16.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy; multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: CeruleanFP; EGFP; VenusFP; tdTomatoFP; mCherryFP; second harmonic generation - SHG
Data qualification: Processed
description: The picture represents a 3D-reconstruction (using Imaris software) of confocal/multiphoton images collected through the thickness (100 micrometers) of the live skin from a bone-marrow transplanted mouse. Cells marked by five fluorescent proteins: Cerulean (cyan), EGFP (green), Venus (yellow), tdTomato (purple), mCherry (red) appear interspersed along reticulin and collagen fibers (second harmonic generation-SHG, white) at 4 months post-transplant. See also Malide et al. (2012) Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy. Blood. Dec 20;120(26):e105-16.
 
This image is grouped with two others obtained in a similar fashion.
DOI: 10.6075/j0zg6qv4
title: CIL:37176, Rattus, glomerular endothelial cell, kidney cell, podocyte. In Cell Image Library

description: Relevant citations: 
Kanwar, Y.S. and M.G. Farquhar. 1979. J. Cell Biol. 81:137-153.
Farquhar, M.G., S.L. Wisssig and G.E. Palade. 1961 . J. Exp. Med. 113:47-66.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification 49,500.
description: Transmission electron micrograph showing normal glomerulus basement membrane filtration slits 15 min post IV ferritin administration. At this time point frerritin is in the capillary lumen basement membrane and none is between the podocytes. The series of images in this group have particular historic and cell biologic importance for determining the role of the glomerular basement membrane in urinary filtration, especially the charge properties and size selectivity in retention of proteins in the circulation. The images here clearly show the glomerular filtration barrier. The study also elucidated the role of the basement membrane in some forms of nephrosis. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: osmium tetroxide fixed tissue
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
DOI: 10.6075/j0kh0m44
title: CIL:36006, Leporidae, simple columnar epithelial cell, mucus secreting cell. In Cell Image Library

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
description: Figure 388 from Chapter 15 (Cytoplasmic Inclusions) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Mucus-secreting cell from a crypt of rabbit colonic mucosa after stimulation in vitro with acetycholine. Experimental stimulation of organ cultures in vitro depletes surface mucus from crypt goblet cells, and leads to exocytosis of centrally-located granules. these events are followed by sequential fusion of successive granules toward the cell center. Image by Marian Neutra and Robert Specian. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
DOI: 10.6075/j09p31rj
title: CIL:36361, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

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.
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: 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
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0cv4gmv
title: CIL:41753, Bacillus thuringiensis. In Cell Image Library

description: Negative staining image of Bacillus thuringiensis, which produces spores and crystals in times of stress. The image was taken using transmission electron microscopy.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: colocated on formvar prepared mesh
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: negative staining
Processing history: unprocessed raw data
DOI: 10.6075/j06w98s9
title: CIL:13591, Mus musculus, myoblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The myoblasts in this image were treated with 300ng/ml insulin-like growth factor II (IGF-II) and 50nM rapamycin (Rap) during differentiation. 0.2 μg/ml follistatin was added to the medium for the last 2 day of differentiation. Follistatin was able to rescue the myotube maturation.

This image is the control of different treatments in Figure 9A from JCB 189: 1157-1169, 2010. See also CIL: 13589, 13590.
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
DOI: 10.5281/zenodo.17489531
title: Pressure-Tunable Band Gap in AlH₃: Toward an Intrinsic Optical Pressure Sensor

description: This record contains WIEN2k_19 calculation data supporting the paper “Pressure-Tunable Band Gap in AlH₃: Toward an Intrinsic Optical Pressure Sensor.” It provides the input and output files corresponding to Figs. 1 and 3, with calculation details described in each directory’s README.md.
DOI: 10.5281/zenodo.17489532
title: Pressure-Tunable Band Gap in AlH₃: Toward an Intrinsic Optical Pressure Sensor

description: This record contains WIEN2k_19 calculation data supporting the paper “Pressure-Tunable Band Gap in AlH₃: Toward an Intrinsic Optical Pressure Sensor.” It provides the input and output files corresponding to Figs. 1 and 3, with calculation details described in each directory’s README.md.
DOI: 10.6075/j09885rz
title: CIL:13593, Mus musculus, myoblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The C2C12 cells stably expressing FLAG-tagged rapamycin-resistant, kinase-inactive (RR/KI) mTOR were induced to differentiate in the presence of 50nM rapamycin (Rap) for 3 days. 25nM TSA was added when the cells were ~60% confluent and removed the next day upon induction of differentiation. TSA was able to rescue the effect of Rap to allow myotube maturation.

This image is the control of different treatments in Figure 9B from JCB 189: 1157-1169, 2010. See also CIL: 13592, 13594, 13601.
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
DOI: 10.6075/j0rx99s1
title: CIL:13592, Mus musculus, myoblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The C2C12 cells stably expressing FLAG-tagged rapamycin-resistant, kinase-inactive (RR/KI) mTOR were induced to differentiation in the presence of 50nM rapamycin for 3 days. The C2C12 cells differentiated, but arrested at the nascent myotube stage.

This image is the control of different treatments in Figure 9B from JCB 189: 1157-1169, 2010. See also CIL: 13593, 13594, 13601.
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
DOI: 10.6075/j07943cd
title: CIL:13650, Homo sapiens. In Cell Image Library

description: This image is Fig. 6A (p125A siRNA). HeLa cells stably expressing ManII-GFP were silenced of p125A and then double labeled using mouse anti-GM130 (secondary Ab: goat anti-mouse Ab labeled with Alexa 633, shown in blue) and rabbit anti-GT (secondary Ab: goat anti-rabbit Ab labeld with Alex 555, shown in red) antibodies followed by viewing the distribution of trans-Golgi marked by GT, medial-Golgi marked by ManII-GFP (shown in green), and cis-Golgi marked by GM130.

Technical details: Cells grown on coverslips were washed 2X with PBS supplemented with 1 mM CaCl2 and 1 mM MgCl2 (PBSCM), fixed with 4% paraformaldehyde in PBSCM for 20 min at RT, washed 5X at 5-min intervals using PBSCM, and then permeabilized with 0.1% Saponin in PBSCM for 20 min at RT. The cells were then immunolabeled with appropriate primary antibodies diluted in fluorescence dilution buffer (FDB; PBSCM with 5% FBS and 2% bovine serum albumin [BSA]) for 1 h at RT, washed 5X with 0.1% Saponin PBSCM at 5-min intervals. Secondary antibodies were diluted in FDB and incubated at RT for 1 h, washed again with 0.1% Saponin PBSCM 5X at 5-min intervals, and then 2X with PBSCM. The coverslips were mounted on microscopic slides with Vectashield mounting medium containing DAPI. Confocal microscopy was performed with an Axioplan II microscope (Carl Zeiss, Inc.) equipped with Zeiss confocal scanning optics. 40x objective.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Green fluorescent proteins from Aequorea; Alexa Fluor 555; Alexa Fluor 633
Data qualification: Raw
DOI: 10.6075/j0765d10
title: CIL:13601, Mus musculus, myoblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The C2C12 cells stably expressing FLAG-tagged rapamycin-resistant, kinase-inactive (RR/KI) mTOR were induced to differentiate in the presence of 50nM rapamycin (Rap) for 3 days. 0.2μg/ml follistatin was added to the medium for the last 2 days of differentiation. Follistatin was able to rescue the effect of Rap to allow myotube maturation.

This image is one of different treatments in Figure 9B from JCB 189: 1157-1169, 2010. See also CIL: 13592, 13593, 13594.
DOI: 10.6075/j0bp01j1
title: CIL:13590, Mus musculus, myoblast. In Cell Image Library

description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The myoblasts in this image were treated with 300ng/ml insulin-like growth factor II (IGF-II) and 50nM rapamycin (Rap) during differentiation. In the presence of both IGF-II and rapamycin, C2C12 cells differentiated into myotubes but arrested at a small myotube size with fewer myonuclei than mature myotubes.

This image is one of different treatments in Figure 9A from JCB 189: 1157-1169, 2010. See also CIL: 13589, 13591.
description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
DOI: 10.6075/j0348j3r
title: CIL:13594, Mus musculus, myoblast. In Cell Image Library

description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The C2C12 cells stably expressing FLAG-tagged rapamycin-resistant, kinase-inactive (RR/KI) mTOR were induced to differentiate in the presence of 50nM rapamycin (Rap) for 3 days. Conditioned medium (CM) was collected daily from parental C2C12 cells that had been induced to differentiate 1 day earlier than the RR/KI mTOR cells and fed to the latter with 50nM Rap added. CM was able to rescue the effect of Rap to allow myotube maturation.

This image is the control of different treatments in Figure 9B from JCB 189: 1157-1169, 2010. See also CIL: 13592, 13593, 13601.
description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.