cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0s182hh
title: CIL:12436, Rattus, multipolar neuron. In Cell Image Library

description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
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 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown 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;spatialmeasurements
DOI: 10.6075/j0fn14wq
title: CIL:12417, Maize mosaic virus, Zea mays, plant cell. In Cell Image Library

description: The images in this group show electron micrographs of epidermal and mesophyll cells in thin sections of maize leaves infected with Maize mosaic virus (MMV, Rhabdoviridae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. This tif image is of a mesophyll leaf cell from a maize plant infected with Maize mosaic virus (MMV), and is identical to the labeled jpg file CIL:16311. MMV virions, budding through the inner nuclear membrane, are accumulating between this membrane and the outer nuclear membrane as well as in intracytoplasmic vesicles, sometimes forming crystalline arrays. 
Detailed methods: Pieces of leaves were processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. See E.-D. Ammar et al. (2005) J. Phytopathology, 153:129-136.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
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; lead salt; uranyl salt
Data qualification: Raw
DOI: 10.6075/j0v69hbc
title: CIL:12416, Maize mosaic virus, Zea mays, plant cell. In Cell Image Library

description: The images in this group show electron micrographs of epidermal and mesophyll cells in thin sections of maize leaves infected with Maize mosaic virus (MMV, Rhabdoviridae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. This tif image is of a mesophyll leaf cell from a maize plant infected with Maize mosaic virus (MMV), and is identical to the labeled jpg file CIL:16309. MMV virions, budding through the inner nuclear membrane, are accumulating between this membrane and the outer nuclear membrane as well as in intracytoplasmic vesicles, sometimes forming crystalline arrays. 
Detailed methods: Pieces of leaves were processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. See E.-D. Ammar et al. (2005) J. Phytopathology, 153:129-136.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
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; lead salt; uranyl salt
Data qualification: Raw
DOI: 10.6075/j0vm49z6
title: CIL:12415, Maize mosaic virus, Zea mays, plant cell. In Cell Image Library

description: The images in this group show electron micrographs of epidermal and mesophyll cells in thin sections of maize leaves infected with Maize mosaic virus (MMV, Rhabdoviridae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. This tif image is of a mesophyll leaf cell from a maize plant infected with Maize mosaic virus (MMV), and is identical to the labeled jpg file CIL:16310. MMV virions, budding through the inner nuclear membrane, are accumulating between this membrane and the outer nuclear membrane as well as in intracytoplasmic vesicles, sometimes forming crystalline arrays. 
Detailed methods: Pieces of leaves were processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. See E.-D. Ammar et al. (2005) J. Phytopathology, 153:129-136.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
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; lead salt; uranyl salt
Data qualification: Raw
DOI: 10.6075/j0pv6kb2
title: CIL:12548, Rattus, multipolar neuron. In Cell Image Library

description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
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 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown 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;spatialmeasurements
DOI: 10.6075/j0r49qrm
title: CIL:12547, Rattus, multipolar neuron. In Cell Image Library

description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
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 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown 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;spatialmeasurements
DOI: 10.6075/j01c1w4g
title: CIL:125, Gallus gallus gallus, erythrocyte. In Cell Image Library

description: Telomeres isolated from chicken erythrocyte nuclei following restriction endonuclease treatment, and imaged by transmission EM after uranyl acetate negative staining. Sample was also labeled for the telomere protein TRF1 using immunogold.
 Image recorded with FEI Tecnai 12 TEM at 100KV and recorded on 2048x2048 CCD with 2x binning.
 Telomeres have a looped conformation, which likely aids in their protection from the rapid degradation that occurs with free DNA ends.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons; charge coupled device (CCD)
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: uranyl salt; uranium compound; gold
Processing history: unprocessed raw image
DOI: 10.6075/j0513z76
title: CIL:12442, Rattus, multipolar neuron. In Cell Image Library

description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
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 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown 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;spatialmeasurements
DOI: 10.6075/j0319v2c
title: CIL:12346, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: elastic scattering of electrons
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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: The plasma membrane of Paramecium multimicronucleatum seen in a freeze fracture replica. The two rows of IMPs can be seen on the P-face of the plasma membrane that connects the plasma membrane to the underlying margins of alveolar sacs. A gap 20nm wide composed of only the plasma membrane connects these two ribbons. The spent vacuole membrane will fuse with the membrane over this gap. Further interpretation of this image can be seen at Figure 4 of Chapter 7 at the link below. TEM taken on 6/3/75 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,750X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j01v5cq7
title: CIL:12401, Leishmania mexicana, Mus musculus, macrophage, protozoan parasites. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin 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
Data qualification: Processed;spatialmeasurements
description: Leishmania mexicana amastigotes in their parasitophorous vacuole in a mouse macrophage. Murine macrophages (cell line J774) were infected in vitro with Leishmania mexicana stationary phase promastigotes (WHO strain MNYC/BZ/62/M379). Four days post infection the cells were fixed with glutaraldehyde, post-fixed with osmium tetroxide, dehydrated in ethanol and embedded in epoxy resin. Thin sections (~90 nm) were viewed on a Philips Technai 12 transmission electron microscope operating at 80 kV. Magnification 2900X.
DOI: 10.6075/j0t152tq
title: CIL:12343, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the cytoproct is the site of spent vacuole defecation on the surface of Paramecium. When closed the cytoproct forms a long narrow wavy ridge along the posterior suture. At its apex the ridge is about 0.2µm wide and it can be as much as 12µm or more in length. This ridge has the ability to be pulled down against the approaching spent vacuole where the plasma membrane covering the midline of the ridge will meet and fuse with the membrane of the vacuole. The ridge contains unique fibers on both of its lips that mesh with each other as they meet inside the ridge (see Allen and Wolf, J. Cell Sci. 14:611-631, 1974). TEM taken on 4/19/79 by R. Allen with Hitachi HU11A operating at 60kV. Neg. 10,000X. Bar = 0.5µm. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: 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
DOI: 10.6075/j0m907ts
title: CIL:12374, Nephrotoma, Nephrotoma suturalis, primary spermatocyte. In Cell Image Library

description: Time series images showing the dynamics of kinetchore microtubules during meiosis I in primary spermatocytes of the crane-fly Nephrotoma suturalis that were experimentally flattened. Time-lapse polarization 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 15 sec using a QImaging Retigo EXi CCD camera. Raw images were processed 
using 5-frame algorithm (Shribak and Oldenbourg, 2003). A movie of the time series is included in this grouped set.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD); Processed image based on 5 recorded images
Imaging mode: polarization microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: intrinsic birefringence
Visualization methods: relative retardation (retardance) measurement
Processing history: 5-frame algorithm
DOI: 10.6075/j0tx3f2m
title: CIL: 53695. In Cell Image Library

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.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j05d8r8v
title: CIL: 51255, 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.