cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09w0d5d
title: CIL:36754, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Acid phosphatase is present in tubules retrieved from late DV-III. The tubules and rounded expansions arising as a result of late DV-III membrane retrieval contain an electron-opaque reaction product when the cells are incubated in Gomori‚Äôs reagent and lead salts. This indicates that acid phosphatase (AcPase) is being retrieved from the late phagolysosomes before the spent vacuole contents are released at the cytoproct. In fact, spent vacuoles no longer contain active AcPase and are free of AcPase-reaction product before they are defecated. (For details of lysosome recycling see Allen and Fok, J. Cell Biol. 99:1955-1959, 1984). TEM taken on 4/27/84 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.2µm. Part published in J. Cell Biol. 99:1955-1959, 1984. Adapted with permission.
description: Preparation: glutaraldehyde 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
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Glutaraldehyde fixation followed by Gomori staining, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This image is suitable for qualitative analysis. A high resolution version of this image in the library (CIL:40566) is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0ms3s9n
title: CIL: 52564, 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=4, z=14 from BL32080_Myc_Terc
DOI: 10.6075/j089153t
title: CIL:1293, 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: 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 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: 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
DOI: 10.6075/j0930s34
title: CIL:27220, Homo sapiens, blood cell, red blood cell. In Cell Image Library

description: Preparation: dispersed cells
Relation to intact cell: whole mounted cells
Item type: recorded image; threshold image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: differences in intrinsic optical density
Visualization methods: visualization of contiguous regions
Processing history: threshold
description: This image set consists of five differential interference contrast (DIC) images of red bood cells (approximately 8 microns in diameter). Each image in the set contains a DIC image and a thresholded image. There are two options when using this data set to quantify an algorithm's effectiveness. The simplest method is simply to compute the percentage of pixels that your algorithm and the thresholded image have in common. However, a wide class of algorithms for handling DIC images do not explicity segment the image, but rather transform the image so that it can later be thresholded. These images were obtained from http://www.broadinstitute.org/bbbc/human_rbc_dic.html

DIC images attributed to Skerker, Rush, and Wiegand; the thresholded images attributed to Morgan.
DOI: 10.6075/j04x57s3
title: CIL:32103, 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/j09s1qhz
title: CIL: 52281, 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=1, z=4 from BL_024216_Myc_Terc
DOI: 10.6075/j0f76b7f
title: CIL:35188, Danio rerio. In Cell Image Library

description: The lateral line primordium is a slug-like mass of cells that crawls down the flank of the fish, leaving clusters of cells that will form the lateral line neuromast organs. Elapsed time indicated by the counters on the left. Video made available by Mark Cooper thru Zebrafish - The Living Laboratory
description: Preparation: living tissue
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
Data qualification: Raw
DOI: 10.6075/j01g0kq1
title: CIL: 51843, 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.
DOI: 10.6075/j0p84bj7
title: CIL: 53489. 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: AGC 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/j0x929cb
title: CIL:2722, Caenorhabditis elegans. In Cell Image Library

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
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.34740/kaggle/dsv/13565383
title: e-IPO Indonesia Data - Investment
DOI: 10.6075/j0j67fw5
title: CIL:2631, 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 12 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/j05m65k5
title: CIL: 54774, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
description: DAPI staining
DOI: 10.6075/j0610xxx
title: CIL:47389, 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 5 - Venular data)
DOI: 10.6075/j0wd406v
title: CIL: 53370, 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: CAMK 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: Visualization methods: confocal microscopy
DOI: 10.6075/j0rf5tgv
title: CIL: 51760, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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/j0j38s91
title: CIL: 54400, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: 14.3 degrees ℃
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 14.3 degrees Celcius
description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
DOI: 10.6075/j0rb73hb
title: CIL:35201, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica 10x NA 0.3 phase contrast objective lens. Images were captured at 3 minute intervals with a Hamamatsu ORCA-ER2 CCD camera using HC Image 2.0.1.11 software.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Movie showing motility and morphology of cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) arrested in G1 using 0.08 uM nocodazole (Uetake and Sluder 2010, Curr Biol 20:1666-1671).
 The time series used to prepare the movie is grouped in the Cell Image Library.
DOI: 10.6075/j04x57xw
title: CIL:39635, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of the double mutant Clb2dbŒî, Clb5Œî, which has the destruction box region of the CLB2 gene, on the cell cycle control system in budding yeast. The yeast, Saccharomyces cerevisia, are growing in 2% raffinose, since this mutation is inviable in glucose. The images from two experiments done with Wild-type Saccharomyces cerevisiae as a control are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0930srn
title: CIL: 52819, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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
description: Tile x=1, y=3, z=17 from PS11_167511L_Myc_Terc
DOI: 10.6075/j06w98wn
title: CIL:40306, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Preparation: glutaraldehyde 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: BY4716 is an auxotrophic haploid laboratory strain of the budding yeast Saccharomyces cerevisiae. Its genotype is lys2Δ, mating type alpha and it is derived from S288c. Sections were embedded in LR white resin, mounted on carbon-coated nickel grids and imaged with LEO 912AB at 80kV and 6,300X. All cells in this batch were grown in liquid rich media (YPD pH6.5) at 30˚C with aerated shaking, and cultures were sampled in mid-logarithmic phase. This image is part of a group of untreated cells and cells exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Transmission electron micrograph of a yeast cell exposed to 60¬µM antidepressant sertraline. This high-magnification zoom of CIL 39708 shows a double-membrane autophagosome. Encapsulated inside the autophagosomes is a multilamellar membrane ‚Äúwhorl.‚Äù