cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0cn737f
title: CIL:41572, Cricetulus griseus, epithelial cell. In Cell Image Library

description: CHO cells at metaphase were treated with 50% D2O, fixed with glutaraldehyde, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranyl acetate and lead citrate for HVEM observation.
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: Preparation: glutaraldehyde 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: uranyl salt; lead salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High voltage (1MeV) transmission electron microscopy image of a 0.5 micrometer section through a Chinese hamster ovary cell at metaphase showing a chromatid pair, with kinetochores at the centromere. The image was taken with a specimen tilt of 63 degrees and is one of a group of 3 tilts from 43 degrees to 63 degrees at 10 degree intervals. Pairs of images provide oblique stereo views of the chromosome.
DOI: 10.6075/j0mg7pn9
title: CIL:46704, Homo sapiens, parenchymal cell. In Cell Image Library

description: Five peroxisomes in a liver parenchymal cell are labeled with gold particles for alanine glyoxylate aminotransferase. Several mitochondria are also shown that are unlabeled. Open spaces contained glycogen that was dissolved.
description: Imaging mode: transmission electron microscopy (TEM)
description: Electron microscopy, immmunocytochemistry on ultra thin section of LRWhite block, after 24 h fixation in buffered formal-calcium, followed by 1h 0.1% glutaraldehyde.
DOI: 10.6075/j07d2tnz
title: CIL: 52387, 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: One z layer of a z-stack at the given tile position
description: Tile x=4, y=5, z=5 from BL024199_Myc_Terc
DOI: 10.6075/j04748pw
title: CIL:35986, Homo sapiens, Sertoli cell. In Cell Image Library

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
description: Figure 365 from Chapter 15 (Cytoplasmic Inclusions) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. These crystalline lattice-like inclusions in human Sertoli cells were first described by Reinke, and are thought to be accumulations of protein, but of unknown function. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
DOI: 10.6075/j0668cfs
title: CIL:1112, Caenorhabditis elegans, muscle cell. In Cell Image Library

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
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.
DOI: 10.6075/j0df6r8m
title: CIL:32084, Homo sapiens, osteocarcenoma. In Cell Image Library

description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0cj8dh3
title: CIL:32069, Homo sapiens, osteocarcenoma. In Cell Image Library

description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
DOI: 10.6075/j0cv4gwf
title: CIL:12070, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution view of the cortex of Paramecium. The proximal end of the basal body is sometimes the origin of other single microtubules or bundles of microtubules that extend deeper into the cell's endoplasm. These guide trichocysts, tip first, to the cell surface and spent vacuoles to the cytoproct. Septal pores connect adjacent alveolar sacs. TEM taken on 1/12/73 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,350X.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/j0j38ss9
title: CIL: 54888, Saccharomyces cerevisiae, Single cell. In Cell Image Library

description: Part of a collage of images of a single nucleolus from yeast strain NOY1051 which has a fixed rDNA array size of 143 repeats. In total 71 of 120 35S ribosomal RNA genes visualized in the Miller chromatin spread from this cell are transcriptionally active. An overview of this nucleolus photographed at low magnification is published in French et al. (2008) Mol Cell Biol. 28:4576-87, Fig. 3A. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447126/figure/f3/
description: Miller chromatin spread. For yeast technique see: Osheim YN, French SL, Sikes ML, Beyer AL. Electron microscope visualization of RNA transcription and processing in Saccharomyces cerevisiae by Miller chromatin spreading. Methods Mol Biol. 2009;464:55-69. doi: 10.1007/978-1-60327-461-6_4. PMID: 18951179.
description: Preparation: Image was captured at a magnification of 6600X on electron microscope film, then enlarged an additional 3.25X when printed onto photographic paper and scanned at 600 dpi.
Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Uranyl acetate; phosphotungstic acid
DOI: 10.6075/j0ww7hsn
title: CIL:40215, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

description: Single computed slice through a tomographic reconstruction of the cell body of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. The reconstruction is the 19th in a series of 26 serial reconstructions through the cell soma. All 26 images can be found in this image group within the Cell Library, and the complete reconstruction can be viewed in the Cell centered database, accession # 7503.
description: Detailed methods can be found at the CCDB link provided. Briefly, one month old male mouse (C57BL/6NHsd) was perfused with Ringer's solution for 2 minutes followed by 2% glutaraldehyde and 2% paraformaldehyde in 0.15M sodium cacodylate buffer, pH 7.4. Further dissection of tissue was followed with postfixation using 1% OsO4, additional staining using 2% uranyl acetate, processed for embedding in durcupan ACM resin, and sectioned at a thickness of 5µm thick. Serial tomograms were produced from single tilt images using a JEOL4000, with 8k x 8k CCD camera, 5000X, 400.0 keV).
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt
Data qualification: Processed
DOI: 10.6075/j02b8xcn
title: CIL:39154, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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 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: A high magnification view of the paracrystalline structure of the trichocyst tip and the cortex and core of the resting trichocyst body. Details of the sheath around the tip spike are also shown. (For details see Bannister, J. Cell Sci. 11:899-929, 1972.) TEM taken on 5/30/69 by R. Allen with Philips 300 operating at 60kV. Neg. 36,500X.
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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0w37vrd
title: CIL: 51233, 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: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
DOI: 10.6075/j0jh3kn8
title: CIL: 52025, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0902398
title: CIL: 52248, Mus musculus, Retinal Pigment Epithelial cells. In Cell Image Library

description: Merged confocal image of mouse (C57BL/6J, postnatal day 720) retinal pigment epithelium (RPE) flatmount. The image is stained for ZO-1 (Green, tight junctions between cells) and nucleus (Red, Propidium Iodide). The RPE cells are in general regularly shaped and arranged polygonal cells, however, their shape and arrangement changes significantly according to their location and age.
description: Imaging mode: confocal microscopy
Visualization methods: primary antibody plus labeled secondary antibody
description: Mouse eye was enucleated, fixed for 10 min in 10% neutral buffered formalin, and washed three times with PBS. Flatmounting was done by making four radial cuts from the center of the cornea back toward the optic nerve. The iris and retina were removed using forceps and additional incisions were made at the ciliary body/cornea margin to relieve tension from the sclera. The RPE flatmounts were stained for rabbit anti-ZO1 antibody (1:100 dilution, catalog no. 61-7300; Invitrogen, Carlsbad, CA) and goat anti-rabbit IgG secondary antibody (catalog no. O11038; Invitrogen). Imaging of the flatmounts was performed with a confocal imaging system (model C1; Nikon) using argon laser excitation at 488 nm. Confocal images were digitally merged (Adobe Photoshop CS2; Adobe, San Jose, CA).
DOI: 10.6075/j0m32v6v
title: CIL: 51887, 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/j0wh2pfj
title: CIL: 51697, 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.