cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0pn94f3
title: CIL:38942, Aggregatibacter actinomycetemcomitans, Gram-negative bacteria. In Cell Image Library

description: Colorized image of a colony of Actinobacillus actinomycetemcomitans, one of the thousands of different types of bacteria found in the mouth. It is one of the main causes of gum disease, which, as well as putting teeth at risk, has been linked with certain kinds of heart disease. The distictive pattern is typical of this type of bacteria and is a result of the conditions under which it is grown. Related images available as CIL:39044, 39045, and 39046.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: modes of light microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: colorized
description: B0007676 Colonies of A. actinomycetemcomitans. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j09022hj
title: CIL:13880, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; boundaries between regions with different refractive index
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tem1-CAAX (green) is targeted away from spindle pole bodies in wild-type cells (this image) but can also still localize to the SPB (CIL# 13881). The CAAX motif from Ras2 targets proteins to the cytoplasmic side of the membrane. tem1Δ::GAL-UPL-TEM1 cells expressing eGFP-TEM1-CAAX from a CEN plasmid were grown on 2% raffinose/2% galactose and transferred to 2% glucose medium prior to image capture. A differential interference contrast (DIC) image is also shown. The tem1Δ::GAL1-UPL-TEM1 strain allows for the rapid, conditional depletion of Tem1. UPL, which stands for ubiquitin-proline-LacI, acts as a destabilizing module that permits rapid degradation of appended proteins. Image is Fig S5D, top panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig S5 include CIL # 13880, 13881.
description: Cells (MATa tem1::GAL-UPL-TEM1-TRP1 pRS316::eGFP-TEM1-CAAX) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
DOI: 10.6075/j02v2f9v
title: CIL:13190, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 1.0 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this low magnification survey micrograph of chromosomes at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde 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: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0qf8sft
title: CIL: 52391, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=5, z=9 from BL024199_Myc_Terc
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
DOI: 10.6075/j0jd4vw2
title: CIL:16243, Mus musculus, pyramidal cell. In Cell Image Library

description: Distribution of hippocampal neurons expressing EGFP from the Nr4a1/Nur77 promoter (Tg(Nr4a1-EGFP)GY139Gsat, www.gensat.org) in hippocampal CA1 colabelled for the vesicular glutamate transporter (VGluT1, red, Invitrogen polyclonal, 1:1000) and stained with DAPI (blue) to show cell layers. EGFP expression was amplified with chicken anti-GFP (Abcam, 1:2000). VGluT1 labels excitatory terminals in the dendritic fields of the pyramidal cells in stratum orien and stratum radiatum. Nr4a1-EGFP is heavily expressed by CA1 pyramidal cells and to a lesser extent in CA3 pyramidal cells with sparse cells in the dentate gyrus (see associated images). Section (40 um, sagittal) was mounted with Fluoromount G and imaged with a 32X, 0.4 NA LD Achroplan objective on a Zeiss Axiovert microscope. AF568 was excited at 562/40 nm and emission collected at 624/40 nm with Semrock filters and a single band dichroic (530-585 nm reflected, 601-800 nm transmitted). AF488 was excited at 482/35 nm and emission collected at 536/40 nm with Semrock filters and a single band dichroic (446-499 nm reflected, 513-735 nm transmitted). DAPI was excited at 350/50 nm and emission collected at 460/50 nm with a CLP400 dichroic (Chroma). Single images were captured for each channel using a Zeiss Axiocam MR CCD and pseudo-colored using Axiovision. Linear background subtraction was used on the presented image. See Davis and Puhl (2011), Pubmed ID 21305052, for a detailed staining protocol and images of EGFP expression in the striatum and amygdala in this strain. This image is part of a series characterizing EGFP expression from the Nr4a1 promoter throughout the brain.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP; Alexa Fluor 488; Alexa Fluor 568
Data qualification: Raw
DOI: 10.6075/j0sq8zh5
title: CIL:16241, Mus musculus, CNS interneuron, hippocampal granule cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP; Alexa Fluor 488; Alexa Fluor 568
Data qualification: Raw
description: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) in the ventral hippocampus colabelled for the CB1 cannabinoid receptor (red) and counterstained with DAPI (blue) to show the cell layers. EGFP expression was amplified with chicken anti-GFP (Abcam, 1:2000); cell bodies and fibers are present throughout all layers of the hippocampus but enriched in the hilus and stratum lacunosum moleculare (see associated images). CB1 immunoreactivity (L15 rabbit polyclonal 1:200, K. Mackie) is prominent in the axon terminals of basket cells synapsing in the pyramidal cell layer. CB1 is also enriched in axons with variable intensity in the inner and outer molecular layer of the dentate gyrus and within the hilus. Lower level CB1 immunoreactivity is also present in the stratum radiatum and stratum oriens. 

Section (40 um) was mounted with Fluoromount G and imaged with a 10X, 0.3 NA objective on a Zeiss Axiovert microscope. AF568 was excited at 562/40 nm and emission collected at 624/40 nm with Semrock filters and a single band dichroic (530-585 nm reflected, 601-800 nm transmitted). AF488 was excited at 482/35 nm and emission collected at 536/40 nm with Semrock filters and a single band dichroic (446-499 nm reflected, 513-735 nm transmitted). DAPI was excited at 350/50 nm and emission collected at 460/50 nm with a CLP400 dichroic (Chroma). Single images were captured for each channel using a Zeiss Axiocam MR CCD and pseudo-colored using Axiovision. Linear background subtraction was used on the presented image. See Davis and Puhl 2011 (Pubmed ID: 21305052) for a detailed staining protocol. This image is part of a series characterizing EGFP expression from the 5HT3 promoter throughout the brain.
DOI: 10.6075/j0s181sp
title: CIL:1624, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 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.
DOI: 10.6075/j00k27j4
title: CIL:36758, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A circular depression on the dorsal surface of the cell marks the expulsion site of a contractile vacuole. This is referred to as the contractile vacuole ‚Äúpore.". Microtubules encircle the pore. Trichocyst tips are pushed to one side by this large opening. Cacodylate buffered fixative. TEM taken on 9/27/68 by R. Allen with Philips 300 operating at 60kV. Neg. 16,000X. Bar = 0.5µm.
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; uranyl salt; lead salt; osmium tetroxide
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. 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:38894) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0rn37bb
title: CIL: 51907, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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/j0bk1cc8
title: CIL:35899, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Lte1. 
 
 LTE1 is essential for termination of M phase at low temperatures, along with TEM1, and CDC15, all part of the mitotic exit network which is an elaborate signaling system comprising at least eight essential genes: CDC5, CDC14, CDC15, DBF2, DBF20, LTE1, MOB1, and TEM1. LTE1 was originally discovered as a locus essential for growth at 8 C, and was named for this trait as Low Temperature Essential 1. It was later inferred from sequence similarities that LTE1 must code for a guanine nucleotide exchange factor. Genetic evidence suggests that Lte1p activates the GTPase Tem1p which activates the protein kinase Cdc15p. Cdc15p then relieves the inhibition of the protein phosphatase Cdc14p by Net1p, thereby allowing exit from mitosis. In a normal cell cycle, Bub2p bound to Tem1p restrains mitotic exit until the daughter-bound centrosome (with which both Bub2p and Tem1p preferentially associate) comes into contact with Lte1p in the bud, effectively coupling mitotic exit with nuclear segregation. Some evidence suggests that the spatial separation of Tem1p and Lte1p is a key mechanism for controlling the timing of mitotic exit.
 
 These phase,gfp images are part of an image group that ranges from CIL:35880-35899. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
DOI: 10.6075/j0kh0m27
title: CIL:40560, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Higher magnification of acidosomes docked at the nascent digestive vacuole membrane. The E-fracture face is relatively IMP free while the P-fracture face has many large IMPs as well as some sizable pits where chunks of this leaflet seem to have stuck to the E-face. Tiny pits on the E-face indicate the removal of individual IMPs from this leaflet. An indentation of the membrane into the lumen of the acidosome shows IMPs on its exposed P-face; which, if any, of these IMPs are V-ATPases is not known. TEM taken on 5/26/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Published in J. Cell Sci. 106:411-422, 1993. Adapted with permission.
description: The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j04b3042
title: CIL:36064, Mus musculus, smooth muscle cell. In Cell Image Library

description: Figure 432 from Chapter 16 (Cytoplasmic matrix and cytoskeleton) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Smooth muscle of mouse epididymal duct. The area within the rectangle is shown at higher magnification in the accompanying image CIL:36065 from this image group, highlighting the presence of actin filaments. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
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
DOI: 10.6075/j0610z3k
title: CIL:39691, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: BY4716 is an auxotrophic haploid laboratory strain of the budding yeast Saccharomyces cerevisiae. Its genotype is lys2Δ, mating type alpha and it is derived from S288c. Sections were embedded in LR white resin, mounted on carbon-coated nickel grids and imaged with LEO 912AB at 80kV and 6,300X. All cells in this batch were grown in liquid rich media (YPD pH6.5) at 30˚C with aerated shaking, and cultures were sampled in mid-logarithmic phase. This image is part of a group of untreated cells and cells exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Transmission electron micrograph of an unbudded yeast cell in which vacuole fission and fusion are apparent. A mitochondrion is faintly discernible above and slightly to the right of the nucleus. A single lipid droplet is also visible in the center of the cell.
DOI: 10.6075/j0z31xms
title: CIL:35559, Cricetulus griseus, ovary. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Colcemid-arrested cells were swollen in hypotonic 75mM KCl, fixed with 4% HCOH, post-fixed with OsO4, embedded in plastic, and 'thick' 0.25 micron sections prepared. Sections were recorded using 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 electron microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Metaphase-arrested CHO cells were swollen in 75 mM KCL, fixed with formaldehyde, post-fixed with OsO4, embedded, and 0.25 micron sections examined by High Voltage EM. Seen is a longitudinal section through a chromatid pair with kinetochore elements. This image recorded with a specimen tilt of 50 degrees is part of a grouped tilt series ranging from 20 degrees to 75 degrees. Pairs providing oblique stereo views of chromosome organization.
DOI: 10.6075/j0ww7gx1
title: CIL:1162, 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 4 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