cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0h41qk5
title: CIL:21745, Drosophila melanogaster, epithelial. In Cell Image Library

description: Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA, CIL 21789) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2, CIL 21749, 21739, 21759, and 21773, respectively) has a different gene knocked down by RNAi. This is the set that were treated with 340 RNAi. There are 10 images of each sample, for a total of 50 images. The images were acquired on a Zeiss Axiovert 200M microscope. A recommended use for these five image sets is to algorithmically compute the number of cells in each image. A tab-delimited text file containing this information can be found at the URL indicated in the attribution box. The recommended citation when using these images is: "We used the Drosophila Kc167 1 image set (Carpenter, et al., Genome Biology, 2006) available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: 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 DNA
Visualization methods: Hoechst 33342
Processing history: unprocessed raw data
DOI: 10.6075/j0sj1jsd
title: CIL:21716, 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: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
description: Quick-freeze deep-etch of the contractile vacuole E-fracture face. This face like the collecting canal membrane is porous indicating that many IMPs have been removed from this leaflet during fracturing. The microtubular ribbon seen here is composed of at least 24 microtubules and is divided into 3 sub-ribbons. Only a few IMPs remain in this leaflet. TEM taken on 6/22/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 24,800X. Bar = 0.2µm.A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:13127) is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0gt5kv6
title: CIL:34917. In Cell Image Library

description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data
description: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
DOI: 10.6075/j0w66k71
title: CIL: 51761, 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/j0222tbx
title: CIL: 52728, 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: Tile x=4, y=3, z=10 from PS11_10021_2B_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0765dvr
title: CIL: 52225, Homo sapiens. In Cell Image Library

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.
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.
DOI: 10.6075/j08g8k7z
title: CIL: 52349, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=3, y=2, z=9 from BL024199_Myc_Terc
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
DOI: 10.6075/j09c6w1h
title: CIL:47677, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

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: 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: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 1)
DOI: 10.6075/j0nz87bd
title: CIL: 53948, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: PKL 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: 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.
DOI: 10.6075/j00g3jqf
title: CIL: 52474, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=5, y=1, z=8 from BL32077_Myc_Terc
description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j06q1w6c
title: CIL:35723, Saccharomyces cerevisiae. In Cell Image 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; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: This is a time lapse image series of Saccharomyces cerevisiae expressing GFP tagged Bub2, a GTPase activator involves in mitotic cell cycle spindle orientation checkpoint and regulation of exit from mitosis. These phase and GFP images are part of an image group containing CIL 35720-35739. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Images were acquired using a 60x 1.42 NA objective lens on a Delta Vision system equipped with a CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j07s7n3d
title: CIL:40389, Helianthus annuus. In Cell Image Library

description: Image collected on a Zeiss DSM 962 SEM. Complete specimen preparation protocol available at:
http://remf.dartmouth.edu:8080/EM-Wiki/36
description: Scanning electron microscope image of cross-section through Helianthus annuus (sunflower) stem. The image shows the outer epidermal layer, followed by the cortex and then large vascular bundles. The vascular bundles have vascular cambium between the phloem (nearest the cortex) and xylem.This image is part of a group on botanical stems (CIL:40378-40395).
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j06972rr
title: CIL:1153, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: 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: 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.
DOI: 10.6075/j0s75g5x
title: CIL: 54813. In Cell Image Library

description: This image displays degenerating neuron with the cristae junction.
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: Item type: recorded image
Imaging mode: Electronic tomography
DOI: 10.6075/j0d50m44
title: CIL:1652, 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 0 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
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/j09c6xgr
title: CIL:32094, Homo sapiens, osteocarcenoma. In Cell Image Library

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
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.
DOI: 10.6075/j0hx1c9c
title: CIL: 53147, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
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 4, z=9 from SC_030
DOI: 10.6075/j07s7nhs
title: CIL: 53960, Homo sapiens, HeLa. In Cell Image Library

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
description: RGC 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.
DOI: 10.6075/j07w6bkm
title: CIL: 50762, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
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/j0xd1116
title: CIL:41704, Cricetulus griseus, ovary. In Cell Image Library

description: Cells were metaphase arrested with colcemid, then exposed to a low ionic strength medium (0.07M phosphate buffer)containing 50% D20 as a microtubule stabilizer. Preparations were squashed in 3:1 acetic acid:ethanol,stained, and transferred to an EM grid.
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: chemically fixed tissue
Relation to intact cell: squash
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High Voltage (1MeV) EM image of metaphase arrested CHO cell squashed in 3:1 acetic acid:ethanol and transferred to an EM grid. Portions of 4 pairs of chromatids are seen. This micrograph was captured at a specimen tilt of 45 degrees. The accompanying image has a tilt of 55 degrees, creating a stereo pair that provides an oblique stereo view of the chromatids.