cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j07p8xtg
title: CIL: 51177, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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.
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: 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
DOI: 10.6075/j00001zd
title: CIL:37080, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

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: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #5 (hour 6) of a developing neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 The cell was imaged daily over 3 days and shows the development of the dendritic arbor and axon over time. This is a second image of this cell at this timepoint.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~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.
DOI: 10.6075/j0wd3zdr
title: CIL:38903, Homo sapiens, epithelial cell of small intestine. In Cell Image Library

description: Confocal image of villi from the human small intestine. The finger-like shape increases the surface area of the intestine, improving the efficiency of food absorption. The intestinal crypts (enzyme secreting glands) can be seen below the villi. The green stain highlights the nucleoli of the rapidly growing epithelial layer of both the villi and the crypts. All the nuclei are stained red and the epithelial cell membranes appear blue.
description: B0006676 Villi from the small intestine. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Processing history: unprocessed raw data
DOI: 10.6075/j00c4tk9
title: CIL:11830, Felis catus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Originally from S. Palay (1976), The Fine Structure of the Nervous System, reprinted with permission as Figure 136 from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the corresponding chapter is available on the ASCB's BioEDUCATE website.
description: Transmission electron micrograph showing the inactive X chromosome (labeled Sex Chromatin), and also known as the Barr body, adpressed to the nucleolus in this section through the nucleus of a spinal cord neuron from a female cat. The inactive X chromosome is typically highly condensed, in keeping with the observation that it is largely inactive in transcription.
description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
DOI: 10.6075/j0jd4wg3
title: CIL: 53702, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
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: CMGC 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/j0g16080
title: CIL: 51771, 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/j08w3cxp
title: CIL: 53056, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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
description: Image 4, z=2 from SC_028
DOI: 10.6075/j09s1q98
title: CIL:686, Zea mays, photosynthetic cell. In Cell Image Library

description: The plastids of plants germinated in the dark are termed etioplasts and possess quasi-crystalline structures termed prolammelar bodies that contain the phospholipid materials and chlorophyll precursors that are converted to green chloroplasts in response to light. The micrograph shows a corn (Zea mays) etioplast fixed after brief exposure to light. The prolamellar body has largely disappeared and thylakoid membranes are starting to form and stack.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: raw unprocessed image
description: Zea mays seeds were germinated in the dark, briefly exposed to light, and segments of coleoptile, excised, fixed with glutataldehyde, post-fixed with osmuim tetroxide, and embedded in epoxy resin. Thin sections were cut, stained with uranyl acetate and lead citrate, and observed using a Philips 300 transmission EM. Images were recorded on film.
DOI: 10.6075/j098869j
title: CIL:1649, 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/j0cn72nd
title: CIL:13093, Acanthamoeba castellanii, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: To characterize and validate the gluteraldehyde fixation method, a live amoeba syringe-loaded with Rhodamine-N58C-profilin-II was monitored in a flow cell as the fixative was introduced. This time series of cooled CCD fluorescence micrographs shows a cell as it is being fixed in 20% Dulbecco's PBS at pH 6.5 containing 1% glutaraldehyde at room temperature. See publication below for details. Live cells were observed with a Zeiss Axiovert 135 fluorescence microscope. Electronic imaging of fluorescent specimens was performed using a Photometrics cooled, charge-coupled device (CCD) camera (PXL-1400) controlled with IPLab Spectrum 3.1P software (Scanolytics, Fairfax, VA) on Macintosh computers. Copyright © 1999 by Company of Biologists and reproduced/adapted with permission in 2011.
description: Preparation: unfixed tissue
Relation to intact cell: living tissue; whole mounted tissue
Item type: absorption of illumination
Imaging mode: UV/visible/IR photons
Parameter imaged: UV/visible/IR illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: fluorescent labels; syringe loaded with Rho-N58C-PII
Processing history: recorded image; intensified CCD (ICCD)
Data qualification: Processed
DOI: 10.6075/j0b56hmt
title: CIL:39106, lung cancer cell. In Cell Image Library

description: Preparation: chemically fixed tissue
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
Processing history: colorized
description: B0007216 Lung cancer cell. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Colorized scanning electron micrograph of a lung cancer cell.
DOI: 10.6075/j06h4gjz
title: CIL:9977, notopthalmus viridescens, erythrocyte. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde 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: tungsten compound
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 paraformaldehyde and negatively stained with 2% sodium phosphotungstate. 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 55 degrees. A grouped image of the same field at a 43 degree tilt provides an oblique stereo view of the tangle of chromatin fibers in the dispersed nucleus.
DOI: 10.6075/j0d21wv6
title: CIL:1664, 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/j01v5cs4
title: CIL:11641, Cavia porcellus, epithelial cell. In Cell Image Library

description: Figure 326 from Chapter 13 (Cilia and Flagella) of 'The Cell' by Don W. Fawcett M.D. Cells of sense organs detecting vibration are provided with stiff surface projections, the size of cilia but lacking their internal structure. The accompanying low-power scanning micrograph presents a surface view of the organ of Corti in the third turn of the guinea-pig cochlea. Three rows of outer hair cells are shown, each bearing a V-shaped array of sensory hairs. The inset shows at high magnification the hairs on two cells from the first row in the second turn of the organ of Corti. Their relative size can be judged by comparison with the microvilli on neighboring cells. These specializations do not arise from centrioles and never contain microtubules. Therefore, they cannot be regarded as modified cilia, but appear to be a unique specialization for mechanoelectrical transduction. A copy of the chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; critical_point dried specimen; whole mounted tissue; shadowing and plating
Relation to intact cell: whole mounted tissue
Item type: scanning electron microscopy (SEM); illumination by electrons
Imaging mode: secondary_electron imaging; film
Parameter imaged: secondary electron generation; secondary_electron imaging
Source of contrast: coherent illumination; secondary electron generation
Visualization methods: shadowing and plating
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j08g8k6h
title: CIL: 52155, Homo sapiens. In Cell Image Library

description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
DOI: 10.6084/m9.figshare.30497123
title: Additional file 1 of Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.30497123.v1
title: Additional file 1 of Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome

description: Supplementary Material 1.
DOI: 10.6075/j0sn089g
title: CIL:38831, 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: High resolution image of Colpoda. A soil ciliate and this micrograph is characterized by numerous mucocysts and food vacuoles containing bacteria in various stages of digestion. This electron micrograph is near the posterior end of the cell and contains spongiome tubules of the contractile vacuole. Rows of cilia cover the cell and basal body/cilium complexes are present as dikinetids, two complexes in each cortical unit. TEM taken on 5/31/69 by R. Allen with Philips 300 operating at 60kV. Neg. 5,000X. The raw film was scanned with an Epson Perfection V750 Pro. This high resolution image is suitable for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0jm289q
title: CIL:37407, Danio rerio, deep cell. In Cell Image Library

description: Zebrafish embryo at 75% epiboly. The view is from the animal pole. The focal plane is deep within the blastoderm. The focal plane changes as the embryo rolls during the sequence. The fluorescent lipid outlines the boundaries of every deep cell in the embryo. Deep cells undergo radial intercalation to form a coherent sheet known as the hypoblast. During embryonic shield formation, cells within the hypoblast migrate towards the embryonic midline (to the upper right of the image.) The dark centers which come into view are nuclei located within the yolk syncytial layer. The rudiment of the head (the head anlagen) emerges as the leading edge of the embryonic shield. The embryo rolls once again. The sequence ends with a cross-sectional view of the enveloping layer ensheathing the embryo. The head anlage lies between the enveloping layer epithelium and the brightly labelled yolk cell.This video made available by Mark Cooper thru Zebrafish - The Living Laboratory. The videos in this group can also be found in the Developmental Landmarks page of the Fishscope web site.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: visualization of contiguous regions; fluorescent lipid
Processing history: unprocessed raw data
Data qualification: Raw