cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0z0387q
title: CIL:10204, Rattus, multipolar neuron. 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: 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
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.
DOI: 10.6075/j0vt1rbf
title: CIL:2305, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 6 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0st7nf6
title: CIL:47670, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - CDB18 A4 block)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
DOI: 10.6075/j0jh3m79
title: CIL:2986, Rattus, multipolar neuron. 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: fluorescence microscopy
Parameter imaged: fluorescence emission
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: Development of the axon and dendritic arbors in cultured hippocampal neurons after 5 days in vitro. MAP2 staining (red) highlights the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Neurons at 2, 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), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 20X (Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Image generated with the MetaMorph color combine function.
DOI: 10.6075/j0nc609f
title: CIL:10010, Didinium nasutum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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;spatialmeasurements
description: Toxicysts, extrusive organelles, (sometimes called extrusomes in protistan lingo) in the proter (or anterior daughter) of a dividing cell. Toxicysts can be very long and are aligned along microtubular lamellae that extend from the cytopharynx. Extra myelin-like membrane can be seen bordering two of the three toxicysts shown. At the upper right is the fibrous cortex of Didinium with mucocysts, an extrusive organelle involved when cyst formation occurs. A digesting food vacuole is at the lower left. TEM taken on 5/20/69 by R. Allen with Philips 300 operating at 60kV. Neg. 6,370X. Bar = 1.0µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution versions of this image (CIL:4667 & 7313) are 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/).
DOI: 10.6075/j0xd10t3
title: CIL:10008, Didinium nasutum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: film; Print from negative scanned for Photoshop.
description: Toxicysts in the cytoplasm of cross sectioned non-dividing Didinium. Toxicysts (extrusomes) are multilayered cylinders that are discharged from the cytopharynx region during capture of prey such as Paramecium. Lipid is stored as large non-membrane enclosed dense bodies in the cytosol. TEM taken on 2/18/69 by R. Allen with Philips 300. Neg. 20,500X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:9929) 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/).
DOI: 10.6075/j09z940z
title: CIL:10007, Didinium nasutum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: An image of one of several contractile vacuole pores of the proter of a dividing cell. This is presumably at an early stage of development as division is not yet complete. This section shows the pore to be encased in microtubules. The micrograph shows the microtubules cut transversely on one side so one can count them and obliquely on the other side of the pore. Whether the CV is yet functional at this stage is not known although the pore septum appears as two flaps of membrane. The pore lies close to the division furrow in the proter. TEM taken on 5/21/69 by M. Sage with Philips 300 operating at 60kV. Neg. 14,800X.Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:4666) 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/).
DOI: 10.6075/j0d799jw
title: CIL:2856, Colpoda cucullus, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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;intensitiesquantitation
description: A high resolution image that shows a dikinetid which is set in a shallow basin in the cell surface. The pair of basal bodies have a proximal cartwheel and a dense septum (not found in most bbs) just distal to the cartwheel. The terminal plate separates the basal body from the cilium that arises from the distal end of the basal body. TEM taken on 5/31/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. The raw film was digitized by scanning with a Nikon Coolscan 9000ED. This image is suitable for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections were prepared at approximately 75nm thickness. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j05h7g2h
title: CIL:36845, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #7 (60 minutes) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with 10 minute intervals and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
 
 Images were acquired every 10 minutes for 1 hour. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~1.5 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j0kd1wx3
title: CIL:2821, Caenorhabditis elegans. In Cell Image Library

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 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: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.15468/dl.w54gxd
title: Occurrence Download

description: A dataset containing 170 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris)",
 "TaxonKey is Isoberlinia"
 ]
}

 The dataset includes 170 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009634-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0319v0g
title: CIL:10081, Notopthalmus viridescence, erythrocyte. In Cell Image Library

description: Nucleated erythrocytes from the newt Notopthahmus viridescens were spread on water, the dispersed chromatin picked up on carbon-formvar grids, fixed with paraformaldehye, critical point dried and shadowed with platinum. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph, the grid was tilted to 55 degrees. A similar micrograph tilted to 45 degrees providing a stereo pair with an oblique 3D view of the tangled and irregular chromatin fibers is grouped with this image.
description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread preparation
Item type: charge coupled device (CCD)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0zp45d0
title: CIL:1008, 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: 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 1 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: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
DOI: 10.6075/j0154g7x
title: CIL:1007, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 1 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: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
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.
DOI: 10.6075/j05x2845
title: CIL:10061, Mus musculus, tracheal epithelial cell. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: detergent permeabilized
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific nucleic acid sequence
Visualization methods: primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 488; Alexa Fluor 594; Cy5
Processing history: unprocessed raw data
description: Mouse tracheal epithelia cells (MTEC) were grown at air-liquid interface to induce differentiation, centriole amplification and ciliogenesis. Cells were fixed with ice-cold methanol for 10 min. Samples were stained with antibodies against acetylated tubulin to mark cilia (red), the centriolar protein Cep120 to mark basal bodies (green), and anti-ZO-1 to mark the cell-cell junctions (light blue). Secondary antibodies were Alexa 594 for acetylated tubulin, Alexa 488 for Cep120, and Cy5 for Zo-1. Nuclei were stained using DAPI (blue). Images were captured using Openlab 4.0.4 software controlling an Axiovert 200M microscope (Carl Zeiss, Inc.) with a 100X 1.4 NA objective.
DOI: 10.6075/j02j6b1f
title: CIL:10104, Homo sapiens, epithelial cell. 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: distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; Fluorescein (FITC)
Processing history: unprocessed raw data
description: Cultured retinal pigment epithelial cells immunofluorescently labeled for transferrin receptor (TfnR) (green) and nucleus (blue). The cells were fixed in 2% PFA and 0.5% Triton X-100 for 2 minutes followed by post-fixation 4% PFA. TfnR was detected with H68.4 primary antibody and secondary FITC antibody. The nucleus was detected with DAPI staining. Images were collected on an Olympus IX-71 epifluorescence microscope using a 100X 1.4 NA objective with 4.500ms exposure for TnfR and 50ms exposure for DAPI (67nm/pixel).