cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0ff3r1n
title: CIL:13400, Xenopus laevis laevis. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
description: A normal X. laevis blastomere expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). Single microtubules extend to the cortex, even in these large cells. X. laevis embryos were imaged on a laser scanning confocal microscope (1024; Bio-Rad Laboratories) mounted on an Axiovert microscope (Carl Zeiss, Inc.) using a 63× 1.4 NA Plan-Apochromat oil objective. Video corresponds to Supplementary Figure 1D and Video 2 from J Cell Biol. 2009 Dec 14;187(6):831-45.
DOI: 10.6075/j05h7fwv
title: CIL: 53174, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 5, z=15 from SC_030
description: One z layer of a z-stack at the given image
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j07d2szk
title: CIL:10817, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde 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; osmium tetroxide
Data qualification: Processed
description: Figure 196 from Chapter 5 (Endoplasmic Reticulum) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A thin section through tibialis anterior of the mouse following fixation by glutaraldehyde solution lacking calcium, and postfixation with osmium-ferrocyanide solution. Skeletal tissue prepared this way results in staining of the etracellular space and T-tubules, but not the sacroplasmic reticulum. In this micrograph, two T-tubules can be seen in each sarcomere at the junctions of the A and I bands. Image by Michael Forbes. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0ww7gwk
title: CIL:1069, 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 2 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/j07s7n6r
title: CIL: 51144, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0r78d6c
title: CIL:35379, Homo sapiens, cevical carcinoma. In Cell Image Library

description: High Voltage transmission electron micrograph of human female (HeLa) mitotic chromosomes from metaphase arrested cell swollen in hypotonic medium and recorded at 1 MeV. This image was taken with a specimen tilt of 55 degrees. Grouped with it is an image of the same area at 45 degrees tilt, providing an oblique stereo view of the chromosome.
description: HeLa cells were metaphase-arrested by a 3hr treatment with colcemid, the cells mechanically broken by passage through a 22-gauge needle and exposed to hypotonic 75 mM KCl for 10 min. Samples were fixed with 3:1 methanol:acetic acid, squashed in 45% acetic acid, transferred to a formvar coated grid, critical point dried, and imaged with the Wisconsin HVEM at 1 MeV. See Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246; Ris (1981) Stereoscopic microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Preparation: coagulating-fixative fixed tissue; critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0b56jjb
title: CIL:36835, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is an image of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the 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.
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.
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
DOI: 10.6075/j0j965wh
title: CIL: 52285, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=1, z=8 from BL_024216_Myc_Terc
DOI: 10.6075/j0f76bvh
title: CIL:40293, Rhododendron, pollen. In Cell Image Library

description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
description: Scanning electron micrograph of Rhododendron pollen. These specimens have been acetolyzed to remove cytoplasm and pollenkit in order to reveal the intricate wall structure. This is part of a large image collection of scanning electron micrographs of pollen samples. Images of a particular species are grouped together. However, to find images and groups of images from other species, please search for the the name of the contributor, Louisa Howard.
description: Preparation: acetolysis
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: gold
Processing history: unprocessed raw data
DOI: 10.6075/j08051r3
title: CIL:9690, Paramecium multimicronucleatum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Paramecium multimicronucleatum - Video of the Contractile Vacuole Complex. Profile view of the rounding/relaxing of an in vitro CV. Side view of an in vitro CV of Paramecium spontaneously rounding and relaxing while confined under mineral oil. The isolated CV will continue to round and relax for as long as 30 min if the cytosolic fluid is not diluted too extensively and there is an adequate supply of ATP available. A DVD resolution version of this is available at CIL:10412.
description: Preparation: living tissue
Relation to intact cell: isolated subcellular component
Item type: microscopy; modes of light microscopy
Imaging mode: differential interference contrast microscopy
Parameter imaged: refractive index
Source of contrast: boundaries between regions with different refractive index
Visualization methods: miscellaneous fill
Processing history: film; unprocessed raw data
DOI: 10.6075/j0n015xw
title: CIL: 50814, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Cells were cultured in YPD medium and high pressure frozen in a Wohlwend Compact 3 machine, followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Saccharomyces cerevisiae cells (S228C background) were high pressure frozen and visualized through 
transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates 
nuclear envelope budding events.
DOI: 10.6075/j03j3c5t
title: CIL:1751, 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 2 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.
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/j07w6bwn
title: CIL: 54138. In Cell Image Library

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.
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.
DOI: 10.6075/j08w3dft
title: CIL:39973, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Visualization methods: intracellular filling
Data qualification: Processed
description: Single transmitted light section from a through focus series through a photoconverted medium spiny cell from the neostriatum of a wild type mouse. Flocculent material surrounding the labeled cell is likely photoconverted mitochondria or non-specific debris produced by the photoconversion procedure. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database, where the reconstruction of the entire cell can also be found.
description: Tissue was prepared from a 7 month adult male mouse strain, C57BL/129SvJ. Tissue sections, 100µm, were generated using a vibratome. The entire through series of images were gathered using a Bio-Rad Radiance 2000 with a 40X 0.75 NA.
DOI: 10.6075/j0mc8xx4
title: CIL:35136, Mus musculus, macrophage. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Cells were extracted from a mouse femur and plated in a coverslip bottom well (MatTek) in standard culture media. The Olympus IX 71 microscope had a simple heated stage. Cells were imaged with a 60X N.A. 1.4 phase 3 planapo objective with a Cooke Sensicam QE operated by IP Lab software running on a Dell Windows XP computer.

This picture is one of a series that may be composed into a montage to see a large field of cells interacting while preserving the high magnification. Some of the pixels in this and the neighboring images are saturated.
description: Phase contrast microscopy of living bone marrow derived macrophages. These cells are highly motile and the snapshot catches lamella and ruffles where the cells are protruding and phase dense organelles inside the volumes of the cells.
DOI: 10.6075/j0v987kv
title: CIL: 52361, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=3, y=2, z=21 from BL024199_Myc_Terc
DOI: 10.6075/j0v40tdw
title: CIL:1035, 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/j0fj2fr0
title: CIL:36245, Vorticella convallaria, 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
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: 11 micrographs are views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows 3 food vacuoles (of a total of about 15 in the cell) containing bacteria and part of a trochal band of basal bodies that surrounds the aboral scopular zone where the stalk originates. TEM taken on 4/2/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,150X. Bar = 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:39327) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0m907p0
title: CIL:7353, notopthalmus viridescens, erythrocyte. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: spread nucleus
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: negative staining; uranyl salt
Processing history: unprocessed raw data
description: Newt (Notopthalmus viridescens erythrocytes were isolated in 0.1M KCl, spread on the surface of Na-citrate, picked up on formvar-carbon films, fixed with glutaraldehyde and negatively stained with 2% uranyl acetate. Images were recorded at 40KX and accelerating voltage of 1MeV at the University of Wisconsin HVEM facility.This image was taken with a specimen tilt of 45 degrees. A grouped image of the same field at a 55 degree tilt provides an oblique stereo view of the tangle of chromatin fibers in the dispersed nucleus.
DOI: 10.6075/j0t72gj1
title: CIL:9174, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Sialyl Transferase-EGFP transfected HeLa cells demonstrating the redistribution of the Golgi Apparatus to the Endoplasmic Reticulum upon treatment with Brefeldin A (BFA). 
Images were collected as a 4D time series (z-stack over time). z-stacks of 48 individual timepoints are included in this collection of files as well as the movie SiEGFP_BFA.avi, which is the maximum projection of the z-stacks at the individual time points.

BFA was added according to the following protocol:
Timepoint1: Before addition of BFA 0seconds (8 Z-slices at 1 um apart)
Timepoint2: After addition of BFA 130seconds (8 Z-slices at 1 um apart) 
Timepoint3: 238 seconds (11 Z-slices at 1 um apart) 
Timepoint3 thru Timepoint48: Images captured every 5 seconds (11 Z-slices at 1 um apart at each time point) 

Images were collected on a Carl Zeiss spinning disk confocal with a 63X 1.4 NA objective with 250 ms exposures at 5 s intervals.
description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data