cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0bv7f8s
title: CIL:28751. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.45 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6075/j0222t81
title: CIL: 52342, 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=3, y=2, z=2 from BL024199_Myc_Terc
DOI: 10.6075/j0pc3157
title: CIL:36047, Mammalia. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: electron-dense stain
Data qualification: Processed
description: Figure 411 from Chapter 16 (Cytoplasmic matrix and cytoskeleton) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Microtubules associated with the midbody in telophase of mammalian cell division. This shaft of microtubules is enclosed at midregion by the plasma membrane and connects daughter cells well into interphase. Image by David Phillips. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
DOI: 10.6075/j0348jpc
title: CIL:40301, Rosa rugosa, pollen. In Cell Image Library

description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
description: Scanning electron micrograph of Rosa rugosa (Beach rose) pollen. These specimens have been acetolyzed to remove cytoplasm and pollenkit in order to reveal the intricate wall structure. This is part of a large image collection of scanning electron micrographs of pollen samples. Images of a particular species are grouped together. However, to find images and groups of images from other species, please search for the the name of the contributor, Louisa Howard.
description: Preparation: acetolysis
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
Processing history: unprocessed raw data
DOI: 10.6075/j02r3r2s
title: CIL:44508, 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:43031 and images grouped with it.
DOI: 10.6075/j06d5rsr
title: CIL:11410, Trypanosoma mega. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
description: Figure 230 from Chapter 7 (Mitochondria) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Kinetoplasts are DNA-rich organelles often found near the basal bodies of the flagellum in protozoans such as the trypanosome (shown here in both upper and lower panels). Images by Winston Anderson. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j00001bb
title: CIL:1435, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: electron density
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.
DOI: 10.6075/j01v5ckf
title: CIL:37909, Homo sapiens, epithelial cell. In Cell Image Library

description: Extrusion of an apoptotic cell from an HBE monolayer as shown by confocal Z-series. This set of images shows middle extrusion events (early and late events are CIL# 37908 and 37910). The bioactive lipid sphingosine-1-phosphate (S1P) is produced by dying cells and activates actomyosin contraction in surrounding cells. The apoptotic condensed nucleus is in blue, the actin-myosin ring at the basolateral surface is in red and S1P is in green.
description: To induce apoptosis, cultured monolayers were exposed to 1,200 µJ/cm2 UV254 irradiation and incubated for 2 h before fixation. Cells were fixed with 4% formaldehyde in PBS, permeabilized with 0.5% Triton, blocked and incubated with primary antibody for 1 h (50 µg/ml anti-S1P mAb (LPath Inc.)). Secondary antibody was Alexa Fluor 488 goat anti–mouse IgG. Actin was detected with Alexa Fluor 568–phalloidin (Invitrogen). DNA was detected with 5 µM DRAQ5 (Axxora). Confocal micrographs were obtained using a microscope (TCS SP5; Leica) with a 63x oil lens with an electron-multiplied cooled CCD camera 1,000 x 1,000, 8 x 8 mm2 driven by the IQ software (Andor Technologies). ImageJ was used to stack confocal sections into Z series that were then color combined and reconstructed into 3D image using MetaMorph (GE Healthcare). All images were processed further using ImageJ, Photoshop (Adobe), Illustrator (Adobe), and Quicktime Pro (Quicktime) software. This Z-series corresponds to Fig 4B from J Cell Biol. 2011. 193(4): 667-676
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; phalloidin; DRAQ5
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0kk9bdh
title: CIL: 53444. In Cell Image Library

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.
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.
DOI: 10.15468/dl.32stf9
title: Occurrence Download

description: A dataset containing 332522 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhus typhina, Parthenocissus quinquefolia, Spiraea billardii, Prunus laurocerasus, Rosa rugosa, Spiraea alba, Pistia stratiotes, Solidago gigantea, Rubus armeniacus, Robinia pseudoacacia, Acer negundo, Ailanthus altissima, Alternanthera philoxeroides, Aponogeton distachyos, Arundo donax, Asclepias syriaca, Azolla filiculoides, Baccharis halimifolia, Cabomba caroliniana, Carpobrotus, Cotoneaster horizontalis, Egeria densa, Eichhornia crassipes, Elaeagnus angustifolia, Elodea canadensis, Elodea nuttallii, Fallopia baldschuanica, Fraxinus pennsylvanica, Gymnocoronis spilanthoides, Helianthus tuberosus, Helianthus laetiflorus, Heracleum mantegazzianum, Hydrilla verticillata, Hydrocotyle ranunculoides, Impatiens capensis, Impatiens glandulifera, Koenigia polystachya, Laburnum anagyroides, Lagarosiphon major, Lemna minuta, Lemna turionifera, Limnobium laevigatum, Reynoutria japonica, Myriophyllum rubricaule, Prunus serotina, Parthenocissus tricuspidata, Mahonia aquifolium, Parthenocissus inserta, Spiraea tomentosa, Spiraea douglasii, Reynoutria bohemica, Salvinia molesta, Myriophyllum heterophyllum, Rudbeckia laciniata, Ludwigia grandiflora, Reynoutria sachalinensis, Spiraea salicifolia, Solidago canadensis, Myriophyllum aquaticum, Ludwigia peploides, Zizania latifolia)",
 "Country is Belgium",
 "Year is greater than or equal to 2013",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 332522 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009639-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j02z151m
title: CIL: 52140, Homo sapiens. In Cell Image Library

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: 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: 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/j01g0jzr
title: CIL:37212, Rattus, cardiac muscle cell. In Cell Image Library

description: Preparation: chemically fixed tissue
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: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x12,000.
description: Transmission electron micrograph of longitudinal section of a a rat heart ventricle. Ordered arrays of myofibrils are interspersed with rows of mitochondria. Small, darkly staining glycogen granules are also prominent.
 Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0df6qvt
title: CIL: 53556, Homo sapiens, HeLa. In Cell Image Library

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.
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/j09c6x3t
title: CIL: 53609, Homo sapiens, HeLa. In Cell Image Library

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.
description: Atypical 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/j0sn08z0
title: CIL:6223, Rattus, multipolar neuron. In Cell Image Library

description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
description: 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), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j03t9gv2
title: CIL: 53596, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: Atypical 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: 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/j02n51hn
title: CIL:1302, 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 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.