cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0mg7n45
title: CIL:37193, Plasmodium. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue
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
description: References:
Palade, G.E. 1952. J. Exp. Med. 95:285-298.
Palade, G.E. 1952. Anat. Rec. 114:427-451.
Sabatini, D.D, K. Bensch and R.J. Barrnett. 1963. J. Cell. Bio. 17:19-58. 
Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification X15,000.
description: Transmission electron micrograph of a mitochondria from the protist Plasmodium. The use of osmium tetroxide as a fixative for electron microscopy was first described by Dr. Palade at the Rockefeller. Another major advance in fixation for electron microscopy was done at Yale by David Sabatini who described the use of glutaraldehyde which not only preserved ultrastructure, but enzymatic activities which opened up the possibility of EM localization of enzymatic function in cells. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0pc3263
title: CIL:36903, 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: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

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

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

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #3 (day 2) of a time lapse series contained with in this image group. It shows the dendritic arbor from a neuron in the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired daily over 3 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 This cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
DOI: 10.6075/j02v2g6x
title: CIL:42155, Mus musculus, epithelial cell. In Cell Image Library

description: Representative time-lapse movie of a normal mouse mammary organoid in a 3D collagen I matrix. The cells are expressing td tomato as a membrane marker and eEGFP-actin using a keratin-14 promoter. Images were collected every 10 minutes. This movie is part of a group of movies that include CIL 42151-42168.
description: Preparation: living tissue
Relation to intact cell: mammary organoid
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: tdTomatoFP; EGFP
Processing history: contrast adjusted; confocal stack
DOI: 10.6075/j0ks6rp0
title: CIL:40059, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
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: lucifer yellow; primary antibody plus labeled secondary antibody; Cy5
Data qualification: Processed
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 either 5% aqueous LY in 200 mM KCl. 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 then ready to be immunolabeled. The rabbit anti-EphA4 antibody was provided by Dr. Elena Pasquale (The Burnham Institute, La Jolla, CA). EphA4 was subsequently detected using goat anti-rabbit Cy5. Slices were 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 LY-filled astrocytes.
DOI: 10.6075/j04749w0
title: CIL:6162, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
description: 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 MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 16X PL Fluotar (0.5 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red) to reveal the development of presynaptic contacts along the dendritic arbor.
DOI: 10.6075/j00k28r7
title: CIL:48104, Rattus norvegicus, skeletal muscle cell. In Cell Image Library

description: Rabbit skeletal muscle cells were fixed and immunostained for actin (from Santa Cruz), and DAPI (from Life Technologies). Images were acquired with a 40X (Plan Fluor, NA 0.75) lens, SPOT RT Slider CCD camera and SPOT Basic image capture software. Image generated with the Image J color combine function.
description: Cryopreserved rabbit skeletal muscle cells were revived and stained for actin (in red) to reveal cytoskeleton and DAPI (in blue) to label nuclei.
description: Relation to intact cell: Dispersed cells cryopreserved; revived and cultured in vitro
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Data qualification: Processed
DOI: 10.6075/j09s1pps
title: CIL:37254, Escherichia coli. In Cell Image Library

description: An electron micrograph of a longitudinal thin section of a dividing Escherichia coli bacterium. The centrally located nucleoid is prominent. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: chemically 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: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification X12,000.
DOI: 10.6075/j0kw5dn2
title: CIL:50657, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI)
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Image was acquired with 60x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with red and vascular endothelial cadherin-stained red regions replaced with cyan for clarity.
DOI: 10.6075/j09z9528
title: CIL:47953, Rattus, testis cell. In Cell Image Library

description: Imaging mode: recorded image
Parameter imaged: electron micrograph
description: The electron micrograph shows the electron dense basal body in a testis cell in primary culture.
description: Testes from 15-day-old Sprague-Dawley rats (Sasco, Omaha Neb.) were dissociated in 0.1% trypsin and plated in NCTC-135 in Petri dishes containing cover slips. Cells on cover slips were fixed in 2.5% glutaraldehyde, 1% osmium tetroxide, stained en bloc with uranyl acetate, dehydrated and embedded in Araldite. Sections were taken parallel to the cover slip, stained with uranyl acetate and lead citrate and examined with a Philips 300 transmission electron microscope. Images were captured on film, printed onto photographic paper, digitized with a scanner and processed with Photoshop (Adobe).
DOI: 10.6075/j06m35ms
title: CIL:25381, Maize mosaic virus, Peregrinus maidis, CNS neuron (sensu Nematoda and Protostomia). In Cell Image Library

description: Aggregates of Maize mosaic virus (MMV, Rhabdoviridae) in cells of brain of the insect vector Peregrinus maidis (planthopper, Hemiptera, Delphacidae). Antibodies to MMV identify aggregates (green/yellow fluorescence) that accumulate mainly around the nuclei (red).

Methods: Dissected insect organs were fixed in paraformaldehyde, labeled with primary antibodies to MMV, and with secondary antibodies: Alexa Fluor-488 (green), and later stained with the nuclear stain propidium iodide (red). Whole mounts were examined with confocal laser- scanning microscope (Leica TCS SP).

Associated references: 
Ammar, E.-D. and S. A. Hogenhout, S.A. (2008). A neurotropic route for Maize mosaic virus (Rhabdoviridae) in its planthopper vector Peregrinus maidis. Virus Research 131: 77-85.
Ammar, E.-D. and Nault, L.R. (1985). Assembly and accumulation sites of Maize mosaic virus in its planthopper vector. Intervirology 24: 33-41.
description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; propidium iodide
Processing history: recorded image
Data qualification: Processed
DOI: 10.6075/j0kk99rk
title: CIL:36552, Xenopus laevis, fertilized egg. In Cell Image Library

description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed 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 epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0r78dcm
title: CIL:10729, Nephrotoma, Nephrotoma suturalis, primary spermatocyte. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: differential interference contrast microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: differences in refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Movie of meiosis I and II in primary spermatocytes of the crane-fly Nephrotoma suturalis. 
Time-lapse DIC microscopy using a Nikon 
Microphot SA, equipped for liquid crystal polarized light microscopy 
(LC-PolScope, CRi, Woburn Massachusetts) 60x/1.4 PlanApo oil immersion objective, 1.4 NA oil imm. condenser, with 2.0x zoom lens. Images captured every 30 sec over 320 min using a QImaging Retigo EXi CCD camera. The time series on which the movie is based is included in this grouped set.
DOI: 10.6075/j09g5m80
title: CIL: 51929, 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/j04b315x
title: CIL: 54666, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after Spz3 KD, 18uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocyte after disruption of cortex glial morphology. After knockdown of Spz3, a secreted neurotrophin, we observed aberrant infiltration by astrocytes into the cortex.
DOI: 10.6075/j0416vmq
title: CIL:47663, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Vcam1)
DOI: 10.6075/j0b8585r
title: CIL:4602, Rattus, multipolar neuron. In Cell Image Library

description: Dendritic development in cultured hippocampal neurons after 17 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons to show the extent and complexity of the dendritic arbor at this relatively mature stage of development.
description: 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 MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 20X (Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0w66jss
title: CIL:7409, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2, which appears as bright circles in AFM images, and volume measurements of the complexes suggest that MeCP2 monomers and dimers are present and that MeCP2 binds DNA cooperatively. Other images in the linked set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: Pixel value determine by specimen height
DOI: 10.6075/j0cf9pdd
title: CIL:40696, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: isolated subcellular component
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Chromosomes were isolated from metaphase cells using a non-aqueous protocol, exposed to non-ionic detergent for 2 hr, fixed with formaldehyde, deposited on a carbon-coated grid,stained with uranyl acetate, and critical point dried.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High voltage (1MeV) transmission electron microscopy image of an isolated metaphase chromatid pair from a mouse A9 cell, showing the fibrous structure. The image was taken with a specimen tilt of 45 degrees. Grouped with it is an image with a tilt of 53 degrees, providing a pair that affords an oblique stereo view of the chromosome.