cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0028r6z
title: CIL: 53598, 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/j0rx9bj9
title: CIL: 51845, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: 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
DOI: 10.6075/j09p3131
title: CIL: 51685, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
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.
DOI: 10.6075/j0b27v07
title: CIL: 54266, Homo sapiens, HeLa. 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: 10.6075/j0pn9531
title: CIL: 51745, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j06m36gd
title: CIL: 53603. 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/j0bv7g4d
title: CIL: 52045, 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: 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
DOI: 10.6075/j0222tgq
title: CIL: 54395, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 9.4 degrees Celcius
description: 9.4 degrees ℃
DOI: 10.6075/j0ks6r6q
title: CIL: 53408, Ceratium lineatum, Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Dinoflagellate
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
DOI: 10.6075/j03x8640
title: CIL: 52325, 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=5, y=2, z=6 from BL_024216_Myc_Terc
DOI: 10.6075/j0d50mf5
title: CIL: 51965, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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.
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.
DOI: 10.15468/dl.axcfyr
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dikerogammarus villosus",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 68 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042918-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5c3xdg
title: Occurrence Download

description: A dataset containing 450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dikerogammarus villosus",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 450 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042919-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4wbhf9
title: Occurrence Download

description: A dataset containing 794 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amaranthus blitoides",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 794 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042920-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8rh8dx
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Mexico",
 "GadmGid is MEX.30_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tropidodipsas fasciata"
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042921-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25980281
title: Wetland biodiversity in Aotearoa New Zealand: an eDNA perspective on exotic and non-exotic species

description: Invasive species threaten biodiversity in Aotearoa New Zealand. In wetlands − significant sites that provide an array of ecosystem and cultural services but represent &lt;10% of their original extent − invasive species can affect hydrological function, nutrient regimes and overall ecological functionality. Environmental DNA (eDNA) has emerged as a valuable biomonitoring technique for cataloguing biodiversity and detecting biological incursions, but little is known about how biodiversity varies in wetlands over fine and broad spatial scales. Here, we examined the publicly available eDNA database of Wilderlab New Zealand, retrieving data from 26 sites across the country to characterise taxonomic diversity patterns, including the extent of exotic and non-exotic (native and endemic) species. We found significant spatial variation in biodiversity – even among neighbouring sites – and a pattern whereby all sites had ≥50% exotic species in their total species tally. Our results provide new information on the current state of wetland biodiversity in Aotearoa New Zealand and highlight the value of eDNA databases for generating new insights from publicly shared data. They also emphasise an urgent need for greater resource allocation to conservation and restoration initiatives in Aotearoa New Zealand that will ensure the persistence of treasured native and endemic wetland species.
DOI: 10.6084/m9.figshare.25980281.v1
title: Wetland biodiversity in Aotearoa New Zealand: an eDNA perspective on exotic and non-exotic species

description: Invasive species threaten biodiversity in Aotearoa New Zealand. In wetlands − significant sites that provide an array of ecosystem and cultural services but represent &lt;10% of their original extent − invasive species can affect hydrological function, nutrient regimes and overall ecological functionality. Environmental DNA (eDNA) has emerged as a valuable biomonitoring technique for cataloguing biodiversity and detecting biological incursions, but little is known about how biodiversity varies in wetlands over fine and broad spatial scales. Here, we examined the publicly available eDNA database of Wilderlab New Zealand, retrieving data from 26 sites across the country to characterise taxonomic diversity patterns, including the extent of exotic and non-exotic (native and endemic) species. We found significant spatial variation in biodiversity – even among neighbouring sites – and a pattern whereby all sites had ≥50% exotic species in their total species tally. Our results provide new information on the current state of wetland biodiversity in Aotearoa New Zealand and highlight the value of eDNA databases for generating new insights from publicly shared data. They also emphasise an urgent need for greater resource allocation to conservation and restoration initiatives in Aotearoa New Zealand that will ensure the persistence of treasured native and endemic wetland species.
DOI: 10.15468/dl.va6jzh
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mimosa pigra",
 "Country is Malaysia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 34 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042923-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yzsc45
title: Occurrence Download

description: A dataset containing 14857 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aethia cristatella)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 14857 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042922-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pjpac2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sewellia breviventralis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042924-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzxnss
title: Occurrence Download

description: A dataset containing 2693 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Otiorhynchus sulcatus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2693 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042925-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3uq7g
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mimosa pigra",
 "Country is Myanmar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042926-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.