cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03x86sh
title: CIL:40081, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. 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; distribution of epitope
Visualization methods: Alexa Fluor 568; primary antibody plus labeled secondary antibody; Alexa Fluor 488
Data qualification: Processed
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 Alexa 568. 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 rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. 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 NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM 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.
DOI: 10.6075/j0zp45hb
title: CIL:45912, Homo sapiens. In Cell Image Library

description: Plate 25700 - 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/j01z438r
title: CIL:40973, Drosophila melanogaster, egg. In Cell Image Library

description: Fluorescent micrograph of a Drosophila melanogaster reproductive system highlighting the muscular and neural structure fruitfly ovaries and uterus. The background staining of the eggs in red is a specific function of the mutant fly strain that is pictured here. Seventh Prize, 2011 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
DOI: 10.6075/j0t153r7
title: CIL:40042, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

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
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.
DOI: 10.6075/j0f47n8z
title: CIL:12342, Euplotes sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: A view of the AZM with basal bodies in longitudinal section and cilia sectioned lengthwise. Bunches of microtubules reside below the basal bodies and lie close to the cytopharyngeal vesicles. TEM taken on 8/3/67 by R. Allen with Philips 200 operating at 60kV. Neg. 19,200X. Bar = 0.2µm. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol, and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. There is a high resolution version of this image in the library (CIL:39338) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0d799ms
title: CIL:12337, Euplotes sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: The transition from 3 to 2 rows of cilia can be seen in this view of the AZM. TEM taken on 7/24/67 by R. Allen with Philips 200 operating at 60kV. Neg. 1,370X. Bar = 5µm. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol, and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image is available in the library at (CIL:38890) for qualitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0jh3k9s
title: CIL:12328, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: This group represents a serial series of sections. At the level of this section, numerous food vacuoles, only three cross sectioned cilia remain of the perioral ciliature. TEM taken on 3/12/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,800X. Bar = 2µm. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared thicker to accommodate the series. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j00865dx
title: CIL:36332, Rattus, astrocyte. In Cell Image Library

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.
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
DOI: 10.15468/dl.xqsyz2
title: Occurrence Download

description: A dataset containing 124679 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "Year 2025-2025"
 ]
}

 The dataset includes 124679 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009233-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2xwpuq
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Hevea brasiliensis",
 "Year 2022-2025"
 ]
}

 The dataset includes 87 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009246-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13563300
title: Egypt Gold Prices | Daily Updated
DOI: 10.6075/j00c4thd
title: CIL:13435, Homo sapiens, breast. In Cell Image Library

description: FISH detection of ERBB2 (fluorescein, green) and MYC (rhodamine, red) in normal breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Z-stacks were acquired to cover the thickness of the tissue section with a step size of 0.5 microns in the Z-direction, and subjected to deconvolution using SoftWoRx 3.5.1 software. A maximum intensity projection of the stack is included in this group of images.
Part of this field of view is shown in Fig 1B of Meaburn et al., 2009, J Cell Biol 187:801-812.
description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0mp5213
title: CIL:13434, Homo sapiens, breast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
description: FISH detection of FOLS2 (FRA2; fluorescein, green) and CSF1R (rhodamine, red) in cancerous breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Shown is a maximum intensity projection of the stack. The complete stack is included in this group of images.
Part of this field of view is shown in Fig 1A of Meaburn et al., 2009, J Cell Biol 187:801-812.
DOI: 10.6075/j0rv0ncp
title: CIL: 53527, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: AGC 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/j0gx499c
title: CIL:13432, Homo sapiens, breast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
description: FISH detection of FOLS2 (FRA2; fluorescein, green) and CSF1R (rhodamine, red) in normal breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Z-stacks were acquired to cover the thickness of the tissue section with a step size of 0.5 microns in the Z-direction, and subjected to deconvolution using SoftWoRx 3.5.1 software. A maximum intensity projection of this image stack is shown. The complete stack is included in this image group.
Part of this field of view is shown in Fig 1A of Meaburn et al., 2009, J Cell Biol 187:801-812.