cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j08915cd
title: CIL: 52183, 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/j0gq6xw4
title: CIL:46751, Rattus sp., parenchymal cell. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
description: Peroxisomes are contrasted with DAB at pH 10.5 by their catalase activity, after fixation in buffered formal-calcium. Postfixation in Os04.
description: Peroxisomes proliferating under treatment with nafenopin over 17 days. Reaction product differs between adjacent organelles giving evidence that their content (catalase) is not freely exchanged, as proposed by the reticulum hypothesis. High magnification shows that apposed peroxisomes are actually separated by their membranes. Bar = 0.1 µm.
DOI: 10.6075/j0c53kkc
title: CIL: 54226. In Cell Image Library

description: TKL 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.
description: Visualization methods: confocal microscopy
DOI: 10.15468/dl.km7hqh
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "OccurrenceStatus is Present",
 "TaxonKey is Macaca assamensis"
 ]
}

 The dataset includes 75 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009432-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j09z93n2
title: CIL:12616, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of a cell treated with trifluoperizine (TFP), all stages of endocytosis and movement to the early endosomes and out of the early endosomes can be found. These steps begin at the parasomal sac and ending with an uncoated carrier vesicles ready to pass into the cell's interior. This micrograph is of the oral region. TEM taken on 10/9/87 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Adapted with permission from Fig. 15 published in J. Cell Sci. 101:449-461, 1992. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Following trifluoperizine (TFP), standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue; trifluoperizine (TFP)
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; osmium tetroxide; uranyl salt; lead salt; horseradish peroxidase
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0kd1wj5
title: CIL:36636, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High magnification view of a crushed mitochondrion showing the zipper-like row of 9nm diameter particles on the outer curve of the cristae and the single row of larger particles on the inner curve. There is an average of 1500 particles per square micrometer of 50-nm tubular cristae surface on the outer curve. These particles are thought to be the F1 units of the F1F0 ATP synthases of the mitochondria. The larger particles on the inner curve resemble complex I of the respiratory electron transport chain in size and relative abundance when compared to their relative quantities estimated from biochemical studies in other cells such as beef heart. This shows the highly ordered arrangement of some of the molecules of the oxidative phosphorylation and electron transport systems in Paramecium. TEM taken on 5/6//88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 63,000X. Bar = 0.1µm. This image is suitable for qualitative analysis. There is a high resolution version of this image in the library (CIL:40505) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/). Published in J. Cell Biol. 108:2233-2240, 1989. Adapted with permission.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
DOI: 10.6075/j0gh9gzq
title: CIL:6567, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
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: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and 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 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was 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.

Stereo pair with CIL:6564.
DOI: 10.6075/j0zc81mf
title: CIL:15795, Dendraster excentricus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
description: Single-plane sequences of anucleate, centrosome-containing cytoplasts (sand dollars) expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). This anucleate cytoplast has two centrosomes, farther apart than the distance to the equator. A furrow initiates at the expected time and place, and proceeds to completion. Embryos were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C. Video corresponds to Fig 7b and the second segment of video 6 in J Cell Biol. 2009 Dec 14;187(6):831-45.
DOI: 10.6075/j0r78fc1
title: CIL:46351, Mus musculus, mammary adenocarcinoma. 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: Examples of single cells' dynamics within an advancing monolayer during a wound healing assay. Upon treatment with HGF/SF, cells close to the wound edge begin to accelerate and stretch, deforming to elongated morphology directed toward the wound edge, followed by enhanced directional migration. These changes propagate into deeper cells in the monolayer in what is referred to as "backward propagating waves". This zoomed-in video displays a small region to visualize how single cells respond to these waves.
description: DA3 cells expressing the fluorescent protein mCherry were grown to 90% confluence in wells of 2 cm diameter in DMEM supplemented with 10% heat-inactivated FCS (Gibco-BRL). A scratch was generated using a 200 µl tip, and the cells were incubated with 80 ng ml-1 Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and subjected to time lapse confocal laser scanning microscopy (CLSM-510, Zeiss, Germany) for approximately 26 hrs, with images taken at 14.5 min intervals. The position of each scratch was predefined, and a macro that repetitively positions the microscope on each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence (shown here) was used for the multi-cellular analysis. These results are under review and a reference to full details will be given upon publication.
DOI: 10.6075/j0zg6s9s
title: CIL:35637, 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 Cln2. Cln2 is a G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p).These phase,gfp images are part of an image group that ranges from CIL:35620-35639. 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; differences in amount of elastic light scattering
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/j0542mfd
title: CIL:38923, globlet cell. In Cell Image Library

description: B0006124 Goblet cell. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Colorized transmission electron micrograph of goblet cells packed full of mucous globules (blue). The cells release the globules to provide lubrication and protection to the inner surfaces of the intestine and the respiratory system among others. The mucous globules are condensed inside the goblet cell but expand hugely once they are released, absorbing water within 20 milliseconds. This rapid release occurs in response to lots of different stimuli and allows the mucous to work instantly. The horizontal field width of the sample is 17.3 micrometers.
description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Processing history: colorized
DOI: 10.6075/j0nz8683
title: CIL:28732. 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 0.60 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/j03n2283
title: CIL:23046, Rattus, fibroblast. In Cell Image Library

description: Preferential distribution of plectin in peripheral regions. REF-52 cells were treated with nocodazole to depolymerize MTs and induce collapse of most IFs to the cell center. Electron microscopy of perinuclear cell regions after gelsolin treatment and immunogold (10 nm) labeling for plectin. shows perinuclear intermediate filament bundles are smooth and contain little plectin. Electron microscopy of cytoskeletons was performed as described (Svitkina et al., 1995). Briefly, cells on coverslips were lysed as for light microscopy, treated, with recombinant gelsolin NHz-terminal domain, fixed with glutaraldehyde, tannic acid and uranyl acetate, critical point dried, and coated with platinum and carbon. Image corresponds to Fig 4d from J Cell Biol. 1996 Nov;135(4):991-1007
description: Preparation: glutaraldehyde fixed tissue; glutaraldehyde fixed tissue; tannic acid
Relation to intact cell: platinum replica
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: uranyl salt; shadowing and plating; primary antibody plus labeled secondary antibody; immunogold
Processing history: unprocessed raw data
DOI: 10.6075/j0pz58t8
title: CIL:35427, Mus musculus, oocyte. In Cell Image Library

description: Preparation: living 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 a specific protein
Visualization methods: DsRed
Processing history: unprocessed raw data
Data qualification: Raw
description: Time-lapse images were acquired using a Photometrics CCD camera (CoolSnap HQ2) mounted on a Leica DMI600B microscope using a Leica HC PL APO 20X/0.7 NA objective enclosed in a thermostatic chamber (Life Imaging Services). Immunofluorescence methods can be found in the cited paper and in Brunet S. et al. (1999) J Cell Biol 146: 1–11.
description: Time-lapse microscopy of mouse oocytes expressing YFP-TPX2 (targeting protein for Xenopus kinesin-like protein, xklp2) and injected with a doublestranded siRNA against TPX2, siTPX2-5h. Images were taken every 30 minutes. Times after the resumption of meiotic maturation and germinal vesicle breakdown (GVBD) are indicated in the lower left corner.
 Video S7. Found at: doi:10.1371/journal.pone.0003338.s007
DOI: 10.6075/j0ff3rf1
title: CIL:2777, Caenorhabditis elegans. In Cell Image Library

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
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.
DOI: 10.6075/j0vq3229
title: CIL:45780, Homo sapiens. In Cell Image Library

description: Plate 24594 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.