cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/d3t-mte-vb4
title: Arinia clausa Vermeulen, 1996

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/69t-aec-xes
title: Euspira nitida (Donovan, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/scd-7qc-sjl
title: Euglesa milium (Held, 1836)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eh9-682-jge
title: Vitrea crystallina (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ets-bh8-q0j
title: Ensis siliqua (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.7g2yms
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Polygonatum acuminatifolium"
 ]
}

 The dataset includes 92 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008257-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/0ar-8pv-pbf
title: Acroloxus lacustris (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7ez-e6p-egw
title: Pyramidellidae J. E. Gray, 1840

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3tn-d8s-nkd
title: Monacha cantiana (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pyp-l3n-vep
title: Talochlamys pusio (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5l6-81v-w42
title: Bithynia tentaculata (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5xt-1a6-9zy
title: Macrogastra attenuata lineolata (Held, 1836)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/035-acv-92w
title: Rissoa parva (da Costa, 1778)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/krm-9jz-jja
title: Talochlamys pusio (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p8r-c3y-jw3
title: Ampullaceana balthica (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rn6-z18-6rm
title: Mimachlamys varia varia (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t8r-qkk-mnw
title: Aequipecten opercularis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4lk-est-25z
title: Bithynia leachii (Sheppard, 1823)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/get-h0h-6qc
title: Pecten sulcicostatus G. B. Sowerby II, 1842

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1k5-c93-m42
title: Anisus vortex (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8ta-gyv-gby
title: Mimachlamys scabricostata (G. B. Sowerby III, 1915)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y15-4sf-x4b
title: Ecrobia ventrosa (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r9h-25d-4yh
title: Planorbis planorbis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tcw-6ad-grs
title: Hippeutis complanatus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pkd-7fx-jl7
title: Planorbarius corneus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yc8-krf-58b
title: Perpolita hammonis (Strøm, 1765)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.jr5c4y
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Strigiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((150 -90,180 -90,180 -60,150 -60,150 -90))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001496-251009101135966/datasets/export for details.
DOI: 10.6075/j0zw1jzn
title: CIL:2696, Caenorhabditis elegans. In Cell Image Library

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: 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: 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/j0445kcx
title: CIL:35842, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc15, a protein kinase involves in cytokinesis. These phase and GFPimages are part of an image group containing CIL 35840-35859. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available 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; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j03x85jz
title: CIL:50622, Homo sapiens, monocyte. In Cell Image Library

description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: One of the 2 monocytes contained 3 erythrocytes. The nucleus was compressed by the erythrocyte group. To note would be the presence of aglutinated, lytic groups of erythrocytes.
description: Imaging mode: microscopy
Visualization methods: x100
DOI: 10.6075/j0zg6s33
title: CIL:36977, 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 #4 (30 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 over one hour, 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.
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/j0fb5359
title: CIL: 54859. In Cell Image Library

description: * Karnovsky fixed tissue
* Osmium tetroxide fixed tissue
* Cells in epoxy resin embedment
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: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: osmium tetroxide
DOI: 10.6075/j07d2t1w
title: CIL:38956, melanocyte. In Cell Image Library

description: Confocal micrograph of an isolated melanin-producing cell (a melanocyte) showing the melanosomes (vesicles that hold the melanin granules) in yellow, the actin in red and the microtubules in blue. The melanin gets transferred from the melanocytes to the epidermal cells, giving colour to the skin and hair.
description: 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 epitope
Processing history: unprocessed raw data
description: B0003424 Melanocyte showing melanosomes. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6084/m9.figshare.30498386
title: Rapid evolution promotes defense-strategy divergence in a widespread plant invader

description: Rapid evolution of defense strategies in non-native plants contributes greatly to their invasion success. Many studies have evidenced the reduced resistance in non-native plants following specialist-herbivore release, but how these plants adjust their defense portfolio against generalist herbivores in the introduced range remains poorly understood. Using the widespread plant invader <i>Spartina alterniflora</i> as a model species, we systematically compared three defense strategies against generalist herbivores—constitutive resistance, induced resistance, and tolerance—among its three genetic groups (native populations, high- and low-latitude introduced populations) in a common garden. We found that compared to native populations, introduced populations as a whole exhibited enhanced constitutive resistance and reduced induced resistance, but no significant difference in tolerance. Within each genetic group, native populations tended to allocate resources evenly among the three defense strategies, whereas high- and low-latitude introduced populations invested more in induced and constitutive resistance, respectively. These findings suggest that <i>Spartina</i> has undergone adaptive evolution in defense strategies within just 40 years since its introduction to China, adjusting resource allocation among different strategies in response to varying herbivory pressures. Our study underscores the importance of integrating generalist herbivores and multiple defense strategies to understand the evolutionary dynamics of plant invasions.
DOI: 10.6084/m9.figshare.30498386.v1
title: Rapid evolution promotes defense-strategy divergence in a widespread plant invader

description: Rapid evolution of defense strategies in non-native plants contributes greatly to their invasion success. Many studies have evidenced the reduced resistance in non-native plants following specialist-herbivore release, but how these plants adjust their defense portfolio against generalist herbivores in the introduced range remains poorly understood. Using the widespread plant invader <i>Spartina alterniflora</i> as a model species, we systematically compared three defense strategies against generalist herbivores—constitutive resistance, induced resistance, and tolerance—among its three genetic groups (native populations, high- and low-latitude introduced populations) in a common garden. We found that compared to native populations, introduced populations as a whole exhibited enhanced constitutive resistance and reduced induced resistance, but no significant difference in tolerance. Within each genetic group, native populations tended to allocate resources evenly among the three defense strategies, whereas high- and low-latitude introduced populations invested more in induced and constitutive resistance, respectively. These findings suggest that <i>Spartina</i> has undergone adaptive evolution in defense strategies within just 40 years since its introduction to China, adjusting resource allocation among different strategies in response to varying herbivory pressures. Our study underscores the importance of integrating generalist herbivores and multiple defense strategies to understand the evolutionary dynamics of plant invasions.
DOI: 10.6075/j0q23z9d
title: CIL:2590, Caenorhabditis elegans. In Cell Image Library

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 10 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: 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: 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.
DOI: 10.6075/j04j0dnp
title: CIL: 52412, 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: Tile x=5, y=2, z=9 from BL024199_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
DOI: 10.6075/j0zw1kgs
title: CIL: 52600. 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=2, y=1, z=8 from PS09_20676_2B_Myc_Terc
DOI: 10.6075/j04q7t66
title: CIL:2234, Caenorhabditis elegans. In Cell Image Library

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 6 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: 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
DOI: 10.6075/j0j38rxp
title: CIL:45913, Homo sapiens. In Cell Image Library

description: Plate 25704 - 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/j0ws8s2w
title: CIL:36053, Mammalia, pillar cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: electron-dense stain
Data qualification: Processed
description: Figures 419 (upper) and 420 (lower) from Chapter 16 (Cytoplasmic matrix and cytoskeleton) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Electron micrographs of pillar cells of the mammalian organ of Corti show highly ordered, stable arrays of microtubules. Rows of pillar cells provide support for the hair cells of the inner ear. Image by Hans Engstr√∂m. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
DOI: 10.6075/j0h994gj
title: CIL:706, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with aurothioglucose. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.