cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.gsgusc
title: Occurrence Download

description: A dataset containing 55203 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ginkgo biloba"
 ]
}

 The dataset includes 55203 records from 439 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009166-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0s75g4g
title: CIL:36851, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #12 (second time-lapse set, 40 minutes) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with 10 minute intervals and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
 
 Images were acquired every 10 minutes for 1 hour. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~1.5 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j09886fb
title: CIL: 50903, Saccharomyces cerevisiae (baker's yeast, budding yeast)" Caenorhabditis elegans (roundworm, nematode) Human mast cell line (HMC-1), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type cells were cultured in YPD medium and high pressure frozen in a Wohlwend Compact 3 machine,
 followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. For the immuno-EM, samples were blocked for 2 hours in 1% BSA with 0.1% fish skin gelatine. A 1:50 dilution of the primary antibody ab24609 was used and a 1:150 dilution of the secondary antibody rabbit anti-mouse immunoglobulins (E0433, Agilend/Dako). Another incubation with a 1:70 diluted 10 nm gold-conjugated protein A (E1808, CMC UMC Utrecht) was followed. Finally, samples were post fixed in 2.5% glutaraldehyde for 20 minutes. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead 
citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
description: Wild type Saccharomyces cerevisiae cells were high pressure frozen and embedded in HM20 resin. Samples were then stained for Nuclear Pore Complex (NPC) assosiated proteins with the monoclonal antibody ab24609 (Abcam) and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events. The black gold particles represent the presence of NPC proteins.
DOI: 10.6075/j0028q4n
title: CIL:47601, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP labelled S. aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue)
description: Visualization of neutrophil recruitment in capillaries proximal to S. aureus beads. (Figure 3 - Icam1)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Processing history: Converted from volocity to .avi
DOI: 10.6075/j0st7nmf
title: CIL:13884, Saccharomyces cerevisiae. In Cell Image Library

description: Constitutive targeting of Tem1 to the spindle pole body (SPB) in metaphase cells (this image) and anaphase cells (CIL#13887). tem1Δ::GAL-UPL-TEM1 cells expressing eGFP-BFA1–TEM1 from a CEN plasmid were grown on 2% raffinose/2% galactose. Image shows localization of Bfa1-Tem1 (eGFP, green) in metaphase after cells were transferred to medium with 2% glucose. Tem1 normally localizes preferentially to the SPB that enters the daughter cell during anaphase (CIL# 13882, 13885). Localization of Bfa1 is similar to that of Tem1, but Bfa1 is more stable on the SPB in the daughter cell and more asymmetric than Tem1 in late anaphase. The Bfa1-Tem1 fusion protein localization resembles Bfa1. Nuclear morphology was assessed by DAPI (blue). A differential interference contrast (DIC) image is also shown (gray). The tem1Δ::GAL1-UPL-TEM1 strain allows for the rapid, conditional depletion of Tem1. UPL, which stands for ubiquitin-proline-LacI, acts as a destabilizing module that permits rapid degradation of appended proteins. Image is Fig 1A, bottom panels, in J Cell Biol. (2011) 192: 599-614. Other images in Fig 1 include CIL #13882, 13883, 13884, 13885, 13886, 13887.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa tem1::GAL-UPL-TEM1-TRP1 pRS316::eGFP-BFA1–TEM1) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
DOI: 10.6075/j08s4q3d
title: CIL: 54860. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: osmium tetroxide
description: Lipid droplet interaction with mitochondria and endoplasmic reticulum in inflammatory neutrophils. The sequence of images in different magnifications shows a transversal sections of the neutrophils. Below plasma membrane is possible to identify the types of contacts between lipid droplet, mitochondria, and endoplasmic reticulum. Neutrophil were observed in inflammatory exudate obtained after 6 hours of Leishmania infantum (MCAN/BR/89/BA262)injection into the peritoneal cavity . Cells were fixed using karnovsky reagent, post-fixed with osmium tetroxide, dehydrated in ethanol and embedded in epoxy resin. Thin sections were viewed on a Zeiss 109 transmission electron microscope. Magnifications 120000, 80000, 50000,10000 and 5000.
description: * Karnovsky fixed tissue
* Osmium tetroxide fixed tissue
* Cells in epoxy resin embedment
DOI: 10.6075/j09c6x9h
title: CIL: 54775, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Nestin staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
DOI: 10.6075/j0pz57sd
title: CIL:27229, Fundulus heteroclitus, scale. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; dehydrated in ethanol
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: uranyl salt; lead salt
Processing history: unprocessed raw data
description: Fundulus heteroclitus scales were chemically fixed with 2.5% glutaraldehyde, 2% formaldehyde in 0.1M cacodylate buffer (pH 7.3), then post-fixed in 4% osmium tetroxide and stained en bloc in 1% uranyl acetate. The scales were then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph was imaged using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80 kV.
description: Collagen fibrils and mineralization in the external layer of Fundulus heteroclitus scale. The external layer is the second of three layers closest to the dermis of an elasmoid. It is composed of thin collagen fibrils about 30nm in diameter, which are organized in a loose meshwork. This layer is the first layer to be formed and mineralized. This mineralization is visible in the extracellular material surrounding the collagen fibrils where mineral deposits in the form of needle-like crystals identified to most likely be hydroxyapatite can be found.
DOI: 10.6075/j0p84b4v
title: CIL:1174, 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 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: 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/j0g44nw6
title: CIL:46201, Homo sapiens. In Cell Image Library

description: Plate 20586 - 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.
DOI: 10.6075/j0x066mn
title: CIL: 52791, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=1, y=1, z=10 from PS11_167511L_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0ht2npz
title: CIL:41481, Cricetulus griseus, epithelial cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: CHO cells at metaphase were exposed to 0.07M KCl, fixed with paraformaldehyde followed by OsO4, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranly acetate for HVEM observation.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: High voltage (1MeV) transmission electron microscopy image of a 0.5 micrometer section through a Chinese hamster ovary cell at metaphase showing a chromatid pair, with kinetochores at the centromere. The image was taken with a specimen tilt of 55 degrees and is grouped with one at 40 degrees. The pair provides an oblique stereo view of the chromosome.
DOI: 10.6075/j09z93t9
title: CIL:36518, Xenopus laevis, fertilized egg. In Cell Image Library

description: Preparation: methanol fixed 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 epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
DOI: 10.6075/j0r49qd4
title: CIL: 53279, Homo sapiens, monocyte. In Cell Image Library

description: Joint synovial fluid, centrifugation, May-Grunwald-Giemsa stain
description: Imaging mode: recorded image
Visualization methods: Microscopy photograph
description: Monocyte/macrophage (black arrows) and lymphocyte (gray arrow) karyorhexis
DOI: 10.6075/j0tm78rx
title: CIL:50515, ultrastructural features in AD neurons. In Cell Image Library

description: Item type: recorded image
Imaging mode: serial section TEM
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer‚Äôs disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope. Stereo viewing and computer assisted serial reconstruction techniques were employed to visualize three-dimensional relationships among cytoplasmic components of cortical neurons.
description: We observed several interesting ultrastructural features in AD neurons. These include associations of paired helical filaments (PHF) with the membranes of the nuclear envelope and with ribosomes, differences between the distribution of the Golgi apparatus in neurons containing paired helical filament bundles as compared to neurons without these filaments, and abnormalities in the microtubules of neuronal processes in the vicinity of neuritic plaques.
DOI: 10.6075/j0tx3fd3
title: CIL:36176, 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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density 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 for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
DOI: 10.6075/j08051c5
title: CIL:15796, Dendraster excentricus. In Cell Image Library

description: Single-plane sequences of anucleate, centrosome-containing cytoplasts (sand dollars) three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). This anucleate cytoplast has four centrosomes variously spaced. A deeply ingressing furrow bisects the well-spaced centrosomes; shallow furrows form over closely spaced centrosomes. 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 7c and the third segment of video 6 in J Cell Biol. 2009 Dec 14;187(6):831-45.
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
DOI: 10.6075/j01c1wcm
title: CIL: 52061, Homo sapiens. In Cell Image Library

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.
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: 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.