cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0xp74m3
title: CIL: 53701. In Cell Image Library

description: CMGC 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: 10.6075/j05m654b
title: CIL: 50872, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Treated 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. 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 (S228C background) were treated with 1 mg/ml of the proline analogue azetidine-2-carboxylic acid (AZC) for 30 and 90 minutes. Then, samples were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0tb16gg
title: CIL: 52753, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
description: Tile x=4, y=4, z=14 from PS11_10021_2B_Myc_Terc
DOI: 10.6075/j0sf2vks
title: CIL: 50876, Saccharomyces cerevisiae (baker's yeast, budding yeast), Old S. cerevisiae cells. In Cell Image Library

description: Old Saccharomyces cerevisiae cells were isolated with the use of Streptavidin magnetic beads. Then, isolated old cells were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
description: The cell surface of exponentially growing Saccharomyces cerevisiae cells was labeled with biotin by incubating the cells with 0,5 mg/ml Sulfo-NHS-LC biotin (#21335, Thermo Fisher scientific) for 20 minutes at room temperature. Cells were grown in YPD, harvested prior saturation of culture, and washed in PBS + 0,5% glucose. Biotinylated cells were labeled with 17.5 ug/ml Streptavidin magnetic beads (#21344, Thermo Fisher scientific) for 1.5 hours followed by 3 x 15 min magnetic sorting with PBS + 0,5% glucose washes in between. Another two rounds of growth, streptavidin-labeling, and sorting was performed. The old cells were recovered in YPD for 4 hours before high pressure freezing. Samples were 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. 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: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0h41qvr
title: CIL: 50854, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Treated 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. 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: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Saccharomyces cerevisiae cells (S228C background) were treated with 1 mg/ml of the proline analogue azetidine-2-carboxylic acid (AZC) for 30 and 90 minutes. Then, samples were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
DOI: 10.6075/j0ks6r58
title: CIL: 52953, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Image 4, z=4 from SC_011
description: One z layer of a z-stack at the given image
DOI: 10.15468/dl.xdr62h
title: Occurrence Download

description: A dataset containing 1099 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Artemisia desertorum"
 ]
}

 The dataset includes 1099 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009403-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0cz36ws
title: CIL: 54582, Xenopus Laevis, Entire Organism. In Cell Image Library

description: Video of African clawed frog embryonic development. Video filename format is as follows organism_temperature_batch. Data was collected at 25.1 degrees Celcius
description: Imaging mode: RGB
Visualization methods: Captured on a microscope using a Canon Rebel Ti5/6 or a one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: 25.1 degrees C
DOI: 10.34740/kaggle/dsv/9358331
title: Indonesia News Dataset (2024)
DOI: 10.6075/j02v2fs4
title: CIL: 53605. In Cell Image Library

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.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0p26xfm
title: CIL:40377, Sus scrofa domestica, kidney epithelial cell. In Cell Image Library

description: See: KJ Salaycik et al. 2005. Quantification of microtubule growth and dynamics in wound-edge cells. J Cell Sci 118:4113-4122.
http://jcs.biologists.org/content/118/18/4113.long
description: Time lapse movie of LLCPK cells stably expressing GFP-EB1, a microtubule tip binding protein. GFP-EB1 fluorescence is seen in microtubules and centrosomes which appear to act as microtubule nucleation sites.
 The stack of images used to prepare the movie is included in this group of images.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Data qualification: Processed
DOI: 10.6075/j0j38rw7
title: CIL:40397, Vibrio cholerae. In Cell Image Library

description: Relevant reference: T.J. Kirn, M.J. Lafferty, C.M.P Sandoe and R.K. Taylor, 2000, "Delineation of pilin domains required for bacterial association into microcolonies and intestinal colonization", Molecular Microbiology, Vol. 35(4):896-910

Complete specimen preparation protocol available at http://remf.dartmouth.edu:8080/EM-Wiki

Image collected on a Zeiss DSM 962 SEM
description: Preparation: glutaraldehyde fixed tissue
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 adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Scanning electron microscope image of Vibrio cholerae bacteria, which infect the digestive system.This image is part of an image group that includes CIL:40395-40399.
DOI: 10.6075/j08s4nt0
title: CIL:40423, Saccharomyces cerevisiae, sac1∆∆ mutant. In Cell Image Library

description: Abnormal organelles from a sac1‚àÜ mutant treated with 60¬µM sertraline. This image is a high-magnification zoom of the cell in CIL 40433.This image is part of an image group of cisternae images, CIL: 40417-40423.
description: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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
DOI: 10.6075/j0vm4b4v
title: CIL:40442, Saccharomyces cerevisiae, drs2∆ mutant. In Cell Image Library

description: Transmission electron micrograph of a vacuole from a sertraline-treated drs2‚àÜ mutant cell. This vacuole contains an undigested autophagosomes. This image is a high-magnification zoom of the cell in CIL40424 (25,000X).This image is part of a group of yeast vacuole images (CIL:40437-40448).
description: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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
DOI: 10.6075/j0hq3z76
title: CIL:40379, Solenostemon scutellarioides. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; shadowing and plating
Processing history: unprocessed raw data
description: Image collected on a Zeiss DSM 962 SEM. Complete specimen preparation protocol available at:
http://remf.dartmouth.edu:8080/EM-Wiki/36
description: Scanning electron microscope image of cross-section through a Solenostemon scutellarioidesi (coleus) stem. This image is a high magnification view of CIL 40378 showing x-section through the vascular bundles. This image is also part of a group on botanical stems (CIL:40378-40395).
DOI: 10.6075/j0f47nh3
title: CIL:40378, Solenostemon scutellarioides. In Cell Image Library

description: Scanning electron microscope image of cross-section through a Solenostemon scutellarioidesi (coleus) stem. The image shows the outer epidermal layer, cortex, vascular bundles, and a central pith.This image is part of a group on botanical stems (CIL:40378-40395).
description: Image collected on a Zeiss DSM 962 SEM. Complete specimen preparation protocol available at:
http://remf.dartmouth.edu:8080/EM-Wiki/36
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j01835tg
title: CIL:40373, Drosophila melanogaster. In Cell Image Library

description: Images collected on a JEOL 1010 TEM.
For additional technical details see:
Webber, H.A, Howard, L., Bickeyl, S.E. 2004. The cohesion protein ORD is required for homologue bias during meiotic recombination. JCB Vol 164 (6): 819-829
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide 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: uranyl salt
Processing history: unprocessed raw data
description: Transmission electron microscope image of synaptonemal complex in nuclei of Drosophila germarium cell. This is a higher magnification image of CIL 40371.
DOI: 10.6075/j0b27t52
title: CIL:40440, Saccharomyces cerevisiae, chc1 mutant. In Cell Image Library

description: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Transmission electron micrograph of a vacuole from a sertraline-treated chc1 mutant cell. This vacuole shows evidence of active autophagy. This image is a high-magnification zoom of the cell in CIL 40415 (16,000X).This image is part of a group of yeast vacuole images (CIL:40437-40448). The image contributor encourages Library users to add comments regarding possible causes the separation between the homogenous electron-opaque contents and the mixed opacity contents.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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
DOI: 10.6075/j06q1w4g
title: CIL:40437, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Transmission electron micrograph of a vacuole from a sertraline-treated BY4716 wildtype cell. (16,000X).This image is part of a group of yeast vacuole images (CIL:40437-40448).
DOI: 10.15468/dl.um29gh
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "Geometry POLYGON((-27.11270 -2.95792,35.11270 -2.95792,35.11270 21.95792,-27.11270 21.95792,-27.11270 -2.95792))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Detarium senegalense"
 ]
}

 The dataset includes 155 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009404-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0pz57p2
title: CIL:40436, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Transmission electron micrograph of a representative untreated swa2 mutant cell. SWA2 encodes the yeast homolog of auxilin, which is a co-chaperone that regulates clathrin assembly and disassembly. swa2 mutant cells exhibit a vacuolar fragmentation phenotype. (6,300X). An image of the same mutant following sertraline treatment is available as CIL 40435.
DOI: 10.6075/j05d8rf3
title: CIL: 52995, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 1, z=4 from SC_028
description: One z layer of a z-stack at the given image
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j0639p6q
title: CIL: 51305, 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: 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: ~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.