cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0mw2g2f
title: CIL:27223, Homo sapiens, blood cell, red blood cell. In Cell Image Library

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.
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
DOI: 10.6075/j0bk1b4q
title: CIL:40459, Homo sapiens, glioma. In Cell Image Library

description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
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
Data qualification: Raw
description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met:

The publication and/or presentation are solely for informational and non-commercial purposes.

The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody HPA003230 (shown in green). HPA003230 is a polyclonal antibody against PDIA3 and labels the endoplasmic reticulum. The cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules (red).
DOI: 10.6075/j0s75fr4
title: CIL: 51257, 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/j0s182jz
title: CIL:35867, Saccharomyces cerevisiae. In Cell Image Library

description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged WHI5. WHI5 is a repressor of G1 transcription that binds to SCB binding factor (SBF) at SCB target promoters in early G1; phosphorylation of Whi5p by the CDK, Cln3p/Cdc28p relieves repression and promoter binding by Whi5; periodically expressed in G1.These phase,gfp images are part of an image group that ranges from CIL:35860-35879. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the 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
DOI: 10.6075/j0057dq6
title: CIL:41671, Homo sapiens, glioma. In Cell Image Library

description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met: The publication and/or presentation are solely for informational and non-commercial purposes. The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody HPA000609 (shown in green). HPA000609 is a polyclonal anti-EMD antibody that labels nuclear membrane and endoplasmic reticulum. The cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules (red).
description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
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
DOI: 10.6075/j089151x
title: CIL:12950, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to GOLPH3 (rabbit polyclonal GMx33) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and GOLPH3 (a trans-Golgi associated protein that can also be associated with mitochondria; smaller gold particles) staining. Note that trans‐Golgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
DOI: 10.6075/j09w0dr1
title: CIL:1045, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 1 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: 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/j06w99gp
title: CIL: 50767, Drosophila melanogaster. In Cell Image Library

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
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.
DOI: 10.6075/j00k27tq
title: CIL:347, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Thin section electron microscopy of gastrocnemius (skeletal) muscle from a wild type mouse. Section was stained with warm uranyl acetate stain.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 30,000X magnification.

This image is part of a set of wild type gastrocnemius muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
DOI: 10.6075/j05q4vnm
title: CIL: 52549, 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=7, y=1, z=20 from BL32077_Myc_Terc
DOI: 10.6075/j03777dq
title: CIL:19125, Spiroplasma kunkelii, Zea mays, plant cell, prokaryotic cell. In Cell Image Library

description: Detailed methods: Tissue was processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. Abbreviations: n = nucleus, S = CSS, v = cell vacuole, w = cell wall, xy = xylem.
description: Electron micrograph of corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) in sieve elements and other phloem cells of infected maize roots. CIL:12587, from the same image group, is an unlabeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. Related images are available in the Library form this contributor.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt
Data qualification: Processed
DOI: 10.6075/j02z14rm
title: CIL:1719, 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 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: 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: 10.6075/j0kh0m0b
title: CIL:37331, epidermal cell. In Cell Image Library

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
description: This video shows stationary epidermal cells with copious retrograde flow of actin. Actin-myosin networks initiate at the cell periphery and flow towards the cell body. Even though actin-nucleation and retrograde flow are taking place, the cells remain stationary with respect to their substrata. Video made available by Mark Cooper thru Zebrafish - The Living Laboratory.
DOI: 10.5281/zenodo.17421377
title: HN-LULC

description: The HN-LULC dataset is a pixel-level dataset, which was created by gathering images from the Sentinel. The Iimages weare acquired from Sentinel-2A with Red, Green, Blue, and NIR channels. The labels areis human annotated, which includinge water, urban, meadow, forest, and farmland.
DOI: 10.6075/j0w66jt7
title: CIL:7653, Dictyostelium discoideum, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: Phagocytosis of bacteria by Dictyostelium discoideum amoebae. These Dictyostelium cells are expressing GFP-2FYVE, which binds to phosphatidylinositol 3-phosphate [PI(3)P], and mRFP-LimEdelta, which binds to actin filaments. The bacteria are E. coli that had been incubated with an inhibitor of cytokinesis, producing elongated forms. Phosphoinositides help to confer specific identities to compartments along the endocytic pathway. PI(3)P identifies early endosomes. It associates with phagosomes ~1 minute after uptake and persists as acidification occurs and digestion begins. Note that the long bacteria do not bind the green PI(3)P marker until after they have been fully internalized. The changing morphology of the long bacteria within the labeled phagosomes reveals the action of digestive enzymes. Three successive time series of 100 frames were collected in a single focal plane using a Zeiss LSM510 confocal microscope with a 63x DIC objective lens. The frames are separated by 3.94 seconds. There was a space of 6 seconds between the first two time series and a space of 9 seconds between the second and third time series. The scaling (pixel size) was 0.10 x 0.10 microns. The images were exported as TIFs using Zeiss LSM 5 Image Examiner and saved both as a TIF stack and as an AVI movie (available at CIL:7654) using NIH ImageJ. The movie spans 20 minutes; it plays at 7.5 fps, 30 times actual speed. For related experiments and further details, see Clarke et al., PLoS ONE 5, e8585 (2010).
description: Preparation: whole mounted tissue
Relation to intact cell: whole mounted tissue
Item type: fluorescence microscopy; fluoresence quenching
Imaging mode: recorded image; single-spot confocal microscopy
Parameter imaged: single-spot confocal microscopy
Source of contrast: fluorescence microscopy
Visualization methods: PA-GFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0td9wqm
title: CIL:44503, Canis lupus familiaris, kidney epithelial cell. In Cell Image Library

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
description: Madin-Darby Canine Kidney (MDCK) epithelial cells expressing YFP-membrane were maintained in DMEM supplemented with 5% fetal FCS in a 37°C, 5% CO2 incubator.
Wound healing assay: Cells were grown to 90% confluence in 24-well plates. Prior to scratching, the cells were starved by changing the medium to DMEM plus 0.1% FCS (starvation medium) for 24 hours. The medium was then changed to either fresh starvation medium (control), or starvation medium with 80 ng ml-1 HGF/SF for an additional 2 hours. A scratch of approximately 300 μm in width was generated using a 200 μl tip. The plate was subjected to time lapse microscopy in a stage incubator (OKOLAB, Italy) on a computer-controlled motorized stage of a confocal microscope (CLSM-510, Carl Zeiss, Germany), used in non-confocal DIC mode, with a 10x (NA 0.30) objective. Image acquisition was initiated 2 hours post scratching. Images were acquired every 15.7 minutes for 15 hours. The coordinates of each scratch were predefined, and a macro that repetitively positions the field of view at each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence was used for the analysis.
description: Time series light microscopy images illustrating a wound healing assay. A monolayer of MDCK (Madin-Darby Canine Kidney) epithelial cells is scratched to create a 'wound' about 300 micrometers in width, after which the growth of the cells to fill the wound is monitored by recording images over the course of 15h.This image is part of a group of 12 that includes control cells (CIL:44501, 502, 506, 507, 508) and after addition of Hepatocyte Growth Factor /Scatter Factor (HGF/SF) to activate HGF/SF-Met signaling (CIL:44503, 504, 505, 509, 510). Also in the group are two movies, one control (CIL:44511), and one HGF/SF treated (CIL:44512). For additional wound healing assays see CIL:43401 and images grouped with it.