cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0ks6rkn
title: CIL:10392, 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; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; elastic scattering of photons
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Processed;spatialmeasurements
description: Cultured hippocampal neurons after 23 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red), and PSD95, a scaffolding protein concentrated in the postsynaptic density of excitatory synapses, particularly in dendritic spines (green). 

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 MAP2 (from S. Halpain) with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch) and PSD95 (from NeuroMab, with Alexa488 conjugated secondary, excitation, 496, emission, 519, Invitrogen). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. The merged image was generated by creating a MetaMorph stack file.
DOI: 10.6075/j0m044wv
title: CIL: 51708, 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: ~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: 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/j0930rvk
title: CIL:13762, Rattus norvegicus, pheochromocytoma, adrenal gland cell. In Cell Image Library

description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: cryostat-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Electron micrograph of PC12 cells transfected with AP-3 siRNA. PC12 cells were plated onto aclar film discs (Pella) coated with poly-L-lysine, transfected twice with 50 nM AP-3delta1 siRNA and fixed with 2.5% glutaraldehyde in calcium-/magnesium-free PBS. The discs were washed three times with 0.1 M sodium cacodylate buffer, pH 7.2, and postfixed for 30 min on ice with 1% osmium tetroxide in cacodylate buffer containing 1.6% potassium ferricyanide. The discs were then washed three times with cacodylate buffer, three times with water, incubated with 0.5% uranyl acetate for 30 min (in the dark), and washed again with water. The samples were dehydrated in a graded series of ethanols while progressively lowering the temperature from 4°C to −40°C then embedded in epon resin. After peeling off the aclar, 60-nm sections were cut and viewed in an electron microscope (FEI Tecnai 12; Phillips) at 120 kV, images were captured with a digital camera at 6,800 magnification. Image is Fig 6D right panel (control is Fig 6D left panel (CIL# 13759) of J Cell Biol. 2010. 191: 1173-1187.
DOI: 10.6075/j0g73dt2
title: CIL:39603, Saccharomyces cerevisiae. In Cell Image Library

description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please read the microscopy section of the referenced paper for details before image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cln1. Cln 1 is a cyclin-dependent protein kinase regulator. These phase and GFP z-series images are part of an image group containing CIL 39601-39605. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
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
DOI: 10.6075/j0rv0mc8
title: CIL:13765, Rattus norvegicus, pheochromocytoma, adrenal gland cell. In Cell Image Library

description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: cryostat-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Electron micrograph of PC12 cells transfected with AP-3 siRNA. PC12 cells were plated onto aclar film discs (Pella) coated with poly-L-lysine, transfected twice with 50 nM AP-3delta1 siRNA and fixed with 2.5% glutaraldehyde in calcium-/magnesium-free PBS. The discs were washed three times with 0.1 M sodium cacodylate buffer, pH 7.2, and postfixed for 30 min on ice with 1% osmium tetroxide in cacodylate buffer containing 1.6% potassium ferricyanide. The discs were then washed three times with cacodylate buffer, three times with water, incubated with 0.5% uranyl acetate for 30 min (in the dark), and washed again with water. The samples were dehydrated in a graded series of ethanols while progressively lowering the temperature from 4°C to −40°C then embedded in epon resin. After peeling off the aclar, 60-nm sections were cut and viewed in an electron microscope (FEI Tecnai 12; Phillips) at 120 kV, images were captured with a digital camera at 6,800 magnification. Image is similar to Fig 6C right panel (CIL# 13764) of J Cell Biol. 2010. 191: 1173-1187.
DOI: 10.6075/j0ff3rgg
title: CIL:14965, Mus musculus, CNS interneuron, hippocampal granule cell. In Cell Image Library

description: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) colabelled in red for calretinin (Swant, 1:2000) and counterstained with DAPI (blue) to show the cell layers. EGFP expression was amplified with chicken anti-GFP (Abcam, 1:2000). 5HT3-EGFP expressing cells and fibers are present throughout all layers of the hippocampus but enriched in the hilus and stratum lacunosum moleculare (see associated images). Calretinin immunoreactivity is prominent in fibers within the inner molecular layer of the dentate gyrus and is also present in small EGFP positive bipolar neuronal cell bodies within the hilus and granule cell layer. Calretinin immunoreactive cells belong to an interneuron class that signal to other interneurons. See Freund and Buzaki (Pubmed ID 8915675) for more information on hippocampal interneurons.

Section (40 um) was mounted with Fluoromount G and imaged with a 32X, 0.4 NA LD 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.
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/j0qv3m3h
title: CIL: 52891, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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 9, z=5 from SC_007
description: One z layer of a z-stack at the given image
DOI: 10.6075/j09g5m0d
title: CIL:12909, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to adipophilin (guinea pig anti-adipophilin) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (15 nm anti-mouse, 10 nm anti-guinea pig; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 28,500 X. See Ladinsky and Howell (2007) for more information on methods used.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
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; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets, as indicated by peripheral labeling with adipophilin (smaller gold particles) and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein) staining (larger gold particles). Note that trans‐Golgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
DOI: 10.6075/j06q1vjf
title: CIL: 54838, Conchiformibius steedae, bacteria. In Cell Image Library

description: Imaging mode: confocal microscopy
Visualization methods: fluorescent d amino acids
description: C. steeade septum after consecutive incubation with BADA for 30 minutes and TADA for 30 minutes. Back view of the 3D reconstruction.
description: Leica TCS SP8 X; 63X Plan-Apochromat glycerine objective with a NA of 1.30 and a refraction index of 1.46.
DOI: 10.6075/j0x63mdv
title: CIL: 51752, 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/j0xs5t3x
title: CIL:13764, Rattus norvegicus, pheochromocytoma, adrenal gland cell. In Cell Image Library

description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: cryostat-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Electron micrograph of PC12 cells transfected with AP-3 siRNA. PC12 cells were plated onto aclar film discs (Pella) coated with poly-L-lysine, transfected twice with 50 nM AP-3delta1 siRNA and fixed with 2.5% glutaraldehyde in calcium-/magnesium-free PBS. The discs were washed three times with 0.1 M sodium cacodylate buffer, pH 7.2, and postfixed for 30 min on ice with 1% osmium tetroxide in cacodylate buffer containing 1.6% potassium ferricyanide. The discs were then washed three times with cacodylate buffer, three times with water, incubated with 0.5% uranyl acetate for 30 min (in the dark), and washed again with water. The samples were dehydrated in a graded series of ethanols while progressively lowering the temperature from 4°C to −40°C then embedded in epon resin. After peeling off the aclar, 60-nm sections were cut and viewed in an electron microscope (FEI Tecnai 12; Phillips) at 120 kV, images were captured with a digital camera at 6,800 magnification. Image is Fig 6C right panel (control is Fig 6C left panel--CIL# 13758) of J Cell Biol. 2010. 191: 1173-1187.
DOI: 10.6075/j0cc0znr
title: CIL:2700, 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 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.
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/j0gt5nb9
title: CIL:40172, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling; distribution of epitope
Visualization methods: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Data qualification: Processed
description: Projection through merged optical section series of adjacent hippocampal astrocytes from a 1-week old male rat, injected with Lucifer Yellow (green) and Alexa568 (red) respectively, and immunolabeled for GFAP (blue), imaged with confocal microscopy. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with Alexa 568. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were immunostained and coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image astrocytes.
DOI: 10.6075/j0k93681
title: CIL:13862, Saccharomyces cerevisiae. In Cell Image Library

description: In tem1Δ cells expressing a Cnm67-Tem1 fusion protein, Cdc15-3HA (red) loads prematurely onto spindle pole bodies during metaphase as determined by spindle morphology (tubulin, green) and nuclear morphology (DAPI, blue). The Cnm67-Tem1 fusion protein is constitutively targeted to spindle pole bodies. Compare with control image CIL# 13864. Image is Fig 3C, middle panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 3 include CIL# 13862, 13863, 13864, 13865, 13866, 13867.
description: Cells (MATa tem1::KanMX ura3::eGFP-CNM67–TEM1::URA3 cdc15::CDC15-3HA) grown in rich media with glucose were fixed for 15 min in 3.7% formaldehyde and 0.1 M potassium phosphate buffer, pH 6.4. Cells were then washed twice with 0.1 M potassium phosphate buffer, pH 6.4, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Fixed cells were digested with 0.1 mg/ml zymolyase-100T (US Biological) and 1/10 volume of glusulase (PerkinElmer) at 30C for 15 min, washed once, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Primary antibodies were anti-HA monoclonal antibody (HA.11; 1:500) and anti-tubulin (Abcam; 1:500). Secondary antibodies were: anti-mouse Cy3 (for HA) and anti-rat FITC (for tubulin). Cells were resuspended in DAPI (1 mg/ml). 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.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: HA peptide tag; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; Cy3; Fluorescein (FITC)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation