cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0st7npb
title: CIL:42801, lung cancer. In Cell Image Library

description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: colorized
description: B0008540 Lung cancer cell. Wellcome Images Copyrighted work available under Creative Commons by-nc-nd 2.0 UK: England & Wales, see http://images.wellcome.ac.uk/indexplus/page/Prices.html
description: Colorized scanning electron micrograph of a cell cultured lung cancer cell.This image is part of an image group, CIL 42801-42803, showing several colorized scanning electron micrographs of cell cultured lung cancer cells.
DOI: 10.6075/j0319vrb
title: CIL: 54736, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Cells imaged with bright field.
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: bright field imaging
description: Live cell imaging.
DOI: 10.6075/j0wd4096
title: CIL: 54405, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: 17.2 degrees ℃
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 17.2 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/j0s46qx1
title: CIL:32141, Drosophila melanogaster, epithelial cell. In Cell Image Library

description: Images were acquired using a motorized Zeiss Axioplan 2 and a Axiocam MRm camera, and are provided courtesy of the laboratory of David Sabatini at the Whitehead Institute for Biomedical Research. Each image is roughly 512 x 512 pixels, with cells roughly 25 pixels in diameter, and 80 cells per image on average. 

Algorithms for finding boundaries between adjacent cells may use the union of the manually outlined cells as input. They may also use the manually outlined nuclei as seed regions. This ensures that the algorithms are compared according to their ability to find boundaries betwen adjacent cells, and not the orthogonal problems of segmenting nuclei and distinguishing foreground (cells) from background.

To compare an algorithm's results to the manual outlines, define the relevant boundary pixels as the pixels that are on the boundary found by the algorith and that are not adjacent to any background pixels. For each relevant pixel, compute the Euclidean distance to the corresponding pixel on the manually found outline. Report the percentage of relevant pixels that are within two pixels of the corresponding pixel on the manually found outline.
description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image; hand drawn contour
Imaging mode: fluorescence microscopy
Parameter imaged: distribution of a specific protein; distribution of DNA
Source of contrast: distribution of a specific protein
Processing history: unprocessed raw data; tracing
Data qualification: Raw
description: Drosophila melanogaster Kc167 cells were stained for DNA (to label nuclei, red) and actin (a cytoskeletal protein, to show the cell body, green). Each image is a dual channel fluorescent image followed by a line tracing of the nuclei and a line tracing of the cell boundary. These images are provided as a tool for testing algorithims to find nuclei and the boundaries between adjacent cells.

Chris Gang outlined the nuclei and cells.
Please use the following recommended citation when using this data. "We used the Drosophila Kc167 2 image set (Jones et al., Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications, 2005), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6075/j0p84bzm
title: CIL:10100, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 1 day in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field.
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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 20X lens (HC PL Fluotar, NA 0.5), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500, suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
DOI: 10.6075/j02f7mw9
title: CIL: 50961, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: populations of ~1200 cells plated on glass in standard media were imaged at 37º C in each experiment. A target subpopulation of ~100 cells display a readily observed extended, ruffling leading edge pseudopod . The cells exhibiting these deployed, extended pseudopods were counted in each unit area at 6 timepoints during the 3 hr observation period following rapid addition of drug to its standard working concentration. Altogether, 6 experiments were carried out for each treatment, yielding average timecourses summarizing observations of ~600 polarized cells.

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 a full therapeutic dose at once at t=0.
DOI: 10.6075/j0h131rv
title: CIL: 54193, Homo sapiens, HeLa. In Cell Image Library

description: TK 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
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.
DOI: 10.6075/j0gh9h85
title: CIL:1077, 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 2 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/j07s7nv8
title: CIL:36333, Rattus, astrocyte. In Cell Image Library

description: Male Sprague Dawley rats, 3 weeks of age, were anaesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. Lucifer Yellow. The astrocytes were filled using a 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60x oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 3 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled to produce this maximum intensity projection image.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
DOI: 10.6075/j00z73dc
title: CIL:40125, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Confocal image of dorsal lateral striatum from a wild type mouse, immunolabeled for the vesicular monoamine transporter VMAT2 (red) and the dopamine receptor associated phosphoprotein DARRP32 (green). This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine
Data qualification: Processed
description: Wildtype mouse (C57BL6/129SvJ from Duke University) was perfused with aldehyde fixatives (4% paraformaldehyde + 0.1% gluteraldehyde), sectioned on Vibratome (thickness, 80 µm), and rinsed in phosphate buffered saline (PBS,3 x 10min) and incubated in blocking buffer (PBS, 3% normal donkey serum, 1% fish skin gelatin, 0.3% Triton X-100, 1% bovine serum albumin). Tissue sections incubated on shaker overnight, 4° C in primary antibodies diluted in blocking buffer as follows: anti-VMAT-2; Host = guinea pig; 1:500 (Oncogene, catalog # 503-01-50);
anti-DARPP-32; Host = mouse; 1:500 (BD Transduction Laboratories, catalog #611520). Following 3 x 10' rinses, tissue was incubated for 2hr, RT, on a shaker in secondary antibodies diluted at 1:100 in working buffer (donkey-anti-mouse AF488 [Molecular Probes, Cat #A21202] and donkey-anti-guinea pig RRX [Jackson Immunoresearch Laboratories, Inc]. Following rinses in PBS, sections were mounted on slides with gelvatol. Individual images were gathered using a BioRad RTS 2000 Multiphoton with a Nikon PlanApo objective (N.A. 1.45).
DOI: 10.6075/j03n23fr
title: CIL:36325, Rattus, astrocyte. In Cell Image Library

description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 3 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled to produce this maximum intensity projection image.
description: Male Sprague Dawley rats, 3 weeks of age, were anaesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. Lucifer Yellow. The astrocytes were filled using a 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60x oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
DOI: 10.6075/j0tm79f9
title: CIL:39788, Lytechinus pictus, mesenchymal cell, epithelial cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: gold; visualization of contiguous regions; osmium tetroxide
Processing history: unprocessed raw data
description: Scanning electron microscope image of Strongylocentrotus drobachiensus embryo at the primary mesenchyme blastula stage. Embryo was split open to reveal the outer epithelial layer and the blastocoel cavity at the vegetal pole. At this stage of embryonic development, primary mesenchyme cells are forming (flask shaped cells in the epithelial layer) and beginning to migrate into the blastocoel cavity.This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
description: Images taken on a JEOL 35C SEM. 
Processing protocol:
1. 2% GTA in 75% MBL SW or FilteredSW 
FSW - fix for 1.5hrs. RT.
2. Rinse with 0.1M NaCacodylate buffer pH 7.4
3. 0.5% OSO4 in .075M NaCacodylate buffer pH 7.4 - 30' in the cold
4. Rinse in 0.1M NaCacodylate buffer ph 7.4
5. Dehydrate thru ETOH: 30%, 50%, 70%, 95% for 5 min each
6. 100% - 3 changes - 15' each
7. Critical Point Dry
8. Stick embryos down onto silver paint. Gently crack open with glass needle (pipette drawn out to a fine point).
9. Sputter coat with AuPd.
DOI: 10.6075/j0jw8cqc
title: CIL:39029, Astyanax mexicanus, neuron. In Cell Image Library

description: Confocal micrograph of a blind cavefish embryo at around five days post-fertilisation viewed from the side (lateral view) with an antibody that targets a calcium binding protein (calretinin) shown in green, which highlights different neuronal types and their processes in the nervous system. The cavefish Mexican tetra (Astyanax mexicanus) has a seeing and a blind form; the latter lives in dark environments, and relies on other senses. The blind cavefish has specially adapted traits that its sighted relation (dwelling near the surface) does not. These include a greater number of sensory receptors and taste buds along its body; these taste buds are also more efficient than the equivalent cells in the seeing cavefish. The eyes are still present at this stage of development but they will degenerate naturally during the lifetime of the fish as they live in a dark environment where eyes are redundant. Adult cavefish are blind.
description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: B0007769 Cavefish embryo. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0mc8zjm
title: CIL: 52446, 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=1, y=5, z=1 from BL32077_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0sf2vdj
title: CIL:1180, 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/j01z440k
title: CIL: 52935, 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 2, z=7 from SC_011
DOI: 10.6075/j0vm4bnk
title: CIL: 50764, Drosophila melanogaster. 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: 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: 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.