cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0x63mh6
title: CIL: 52936, 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 2, z=8 from SC_011
description: One z layer of a z-stack at the given image
DOI: 10.6075/j03t9ft6
title: CIL:48832, Mus musculus, MC57-Cerulean. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC57-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the DsRed mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts (absent in the DsRed mouse tumor). Image name: 120513 parab dsred tumor flank.lif - 5 

Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j02v2ftk
title: CIL: 53815, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
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: OTHER 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.
DOI: 10.6075/j0m908sr
title: CIL:40037, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with either 5% aqueous LY in 200 mM KCl. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were then ready to be immunolabeled. The rabbit anti-EphA4 antibody was provided by Dr. Elena Pasquale (The Burnham Institute, La Jolla, CA). EphA4 was subsequently detected using goat anti-rabbit Cy5. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling; distribution of epitope
Visualization methods: lucifer yellow; primary antibody plus labeled secondary antibody; Cy5
Data qualification: Processed
DOI: 10.6075/j09c6w02
title: CIL:45980, Homo sapiens. In Cell Image Library

description: Plate 25993 - 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/j0hx1cp9
title: CIL:36327, Rattus, astrocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
description: Male Sprague Dawley rats, 3 weeks of age, were anaesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. Lucifer Yellow. The astrocytes were filled using a 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60x oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 3 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled to produce this maximum intensity projection image.
DOI: 10.6075/j09023t0
title: CIL:25356, Hydra viridis, epithelial cell. In Cell Image Library

description: Scanning electron micrograph showing tentacles on the head of a Hydra viridis. Epithelial cells located at the base of the tentacle are in a flat, contracted state. Cell distal to the head of the H. viridis are rounded in their relaxed state. Specimens were fixed in Aldehyde-osmium fixative 0.75% glutaraldehyde, 0.75% formaldehyde and 1.0% OsO4 prepared in 0.05M sodium cacodylate buffer. Fixative was buffered to pH 7.4-7.5. H. viridis were critical point dried and sputter coated with gold. Image was taken on a FEI Quanta 200 ESEM scanning electron micrograph. This sample was photographed as a montage at a magnification of 382x and an accelerating voltage of 15kV with a 10.0mm working distance. This image belongs to the image group Hydra viridis_AMiller.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue; formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: scanning electron microscopy (SEM)
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: secondary electron generation
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0p849n5
title: CIL:50606, Homo sapiens, monocyte. In Cell Image Library

description: Imaging mode: microscopy
Visualization methods: x100
description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: The monocyte type cell contained 2 erythrocytes.
DOI: 10.6075/j0gb22mw
title: CIL:49157, Homo sapiens. In Cell Image Library

description: Plate 24655 - 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. 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 experiment consists of 375 plates in 384-well format, for a data set comprised of 988,994 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 approximately 5 million 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 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

The experiment consists of 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.15468/dl.qfxjdj
title: Occurrence Download

description: A dataset containing 716166446 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "CoordinateUncertaintyInMeters 0.0-100000.0",
 "GbifRegion is one of (Africa, Asia, Europe and Central Asia, North America, Oceania, Latin America and the Caribbean, Antarctica)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 716166446 records from 22205 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009335-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/0b7-4q7-1we
title: Scrophularia olympica Boiss.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/k57-ky1-ss7
title: Campanula lyrata Lam.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/mx5-fj4-wb0
title: Nonea versicolor (Steven) Sweet

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/7vt-r2z-vsn
title: Hura crepitans L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/cbv-xap-vpm
title: Limonium angustebracteatum Erben

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/2mr-989-ccj
title: Limonium angustebracteatum Erben

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/th3-bh1-d7v
title: Limonium delicatulum (Girard) Kuntze

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/cdg-bty-a0r
title: Limonium densissimum (Pignatti) Pignatti

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/tgw-6rf-l2v
title: Limonium supinum (Girard) Pignatti

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/v6d-rma-ng8
title: Limonium cossonianum Kuntze

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/3dc-w1c-9bz
title: Plantae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/mtg-yg4-xrg
title: Scheuchzeria palustris L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/pxy-9qx-9tg
title: Limonium cymuliferum (Boiss.) Sauvage & Vindt

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/zp9-3qj-9dd
title: Limonium brassicifolium (Webb & Berthel.) Kuntze

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/a1x-r14-d6w
title: Cupressus sempervirens L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/fg9-nyx-fzy
title: Pontederia crassipes Mart.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qme-lf3-xyj
title: Arenaria saxatilis L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/aw2-82s-2qp
title: Limonium Mill.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/b2f-1qs-fll
title: Limonium pectinatum (Aiton) Kuntze

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/bm6-v7f-v12
title: Limonium aegaeum Erben & Brullo

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/f57-r3q-rqq
title: Limonium pectinatum (Aiton) Kuntze

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jet-mlt-mjj
title: Acanthus spinosus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ylw-kc8-44x
title: Limonium delicatulum (Girard) Kuntze

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/5gq-gbm-wh0
title: Eremogone formosa (Fisch. ex Ser.) Fenzl

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/e5k-p7r-j86
title: Pilgerodendron uviferum (D.Don) Florin

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/sge-cq4-qb0
title: Plantae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/784-r00-apv
title: Juniperus macrocarpa Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/s9v-fj7-qe5
title: Pilgerodendron uviferum (D.Don) Florin

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/2lv-f6q-f06
title: Dianthus corymbosus Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/v8p-5lx-bh5
title: Juniperus oxycedrus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/w8g-01x-men
title: Fitzroya cupressoides (Molina) I.M.Johnst.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/ynz-p73-s8c
title: Dianthus corymbosus Sm.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/h43-vdf-wbe
title: Cephalotaxus harringtonii (Knight ex. J.Forbes) K.Koch

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jhq-dkg-3nk
title: Pilgerodendron uviferum (D.Don) Florin

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/s5n-pr3-djy
title: Acanthophyllum squarrosum Boiss.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dqc-4pm-jkz
title: Austrocedrus chilensis (D.Don) Pic.Serm. & Bizzarri

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/xbc-s2d-ctr
title: Cupressus torulosa D.Don ex. Lamb.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/c53-7vl-7we
title: Austrocedrus chilensis (D.Don) Pic.Serm. & Bizzarri

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/yr5-1hf-wpc
title: Polyscias sambucifolia (DC.) Harms

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/fz2-cd4-nmk
title: Austrocedrus chilensis (D.Don) Pic.Serm. & Bizzarri

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/rec-624-7pw
title: Austrocedrus chilensis (D.Don) Pic.Serm. & Bizzarri

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4ps-xjx-gt8
title: Fitzroya cupressoides (Molina) I.M.Johnst.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/56e-14l-sxp
title: Fitzroya cupressoides (Molina) I.M.Johnst.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/nja-rad-h1c
title: Dianthus L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.