cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0pv6j1m
title: CIL:50351, Mus musculus, Spinal cord neuron. In Cell Image Library

description: Biological samples are frequently stained with heavy metals in preparation for examining the macro, micro and ultra-structure using X-ray microtomography and electron microscopy. A single X-ray microtomography scan reveals detailed 3D structure based on staining density, yet it lacks both material composition and functional information. Using a commercially available polychromatic X-ray source, energy integrating detectors and a two-scan configuration labelled by their energy- High and Low, we demonstrate how a specific element, here shown with iron, can be detected from a mixture with other heavy metals. With proper selection of scan configuration, achieving strong overlap of source characteristic emission lines and iron K-edge absorption, iron absorption was enhanced enabling K-edge imaging. Specifically, iron images were obtained by scatter plot material analysis, after selecting specific regions within scatter plots generated from the High and Low scans. Using this method, we identified iron rich regions associated with an iron staining reaction that marks the nodes of Ranvier along nerve axons within mouse spinal roots, also stained with osmium metal commonly used for electron microscopy.

60kVp with fe filtration.
description: XRM was performed on a Versa 510, (Carl Zeiss X-ray Microscopy, Pleasanton, CA 94588). The Versa 510 is equipped with a polychromatic tungsten source, tunable in the voltage range 30-160kVp. Scan configuration: "Low" -30kVp peak tube potential without filtration, exposure time 20-90sec. "High"-60kVp peak tube potential, filtration 25μm thick iron filter, exposure time 10-120sec. Common scan conditions: binning 1, source-rotation axis distance 7.5mm, detector-rotation axis distance 5mm, pixel size 0.394μm, optical magnification x20, rotation angle -180° to +180°, number of views 3201. Iron filtration used a 0.001"x1"x2" foil placed at the X-ray tube exit slit. The foil was of 3N5 purity and sold by ESPI Metals, Ashland, OR 97520.
description: Item type: recorded image
Imaging mode: X-ray micrograph
Source of contrast: Fe and Os staining
DOI: 10.4121/0876521b-5bf2-447a-bdad-2369352b917b
title: Data accompanying Chapter 3 of the thesis: Enabling ship changeability; a lifecycle approach to the maritime energy transition

description: This collection contains datasets created as part of the doctoral thesis "Enabling ship changeability; a lifecycle approach to the maritime energy transition by Jesper Jan Zwaginga, M. Sc in Delft University of Technology, 2020-2025.<br>It is being made public both as supplementary data for the thesis and for other researchers to use in their own work.<br>The data is part of the project READINESS, project number TWM.BL.019.002, of the research programme“Topsector Water & Maritime: the Blue route,” which is partly financed by the Dutch Research Council (NWO).<br>The dataset included in this repository consists of several zip files that contain relevant data for each method application from chapter 3:1. Chapter 3.1 Exploratory methods: contains data to reproduce figures for the RDM, RSC and DAPP method investigation2. Chapter 3.2 Search methods: contains data to reproduce figures for the SP and ARO method investigation
DOI: 10.6075/j0rf5sp4
title: CIL:50303, Rattus norvegicus, alveolar type II cell. In Cell Image Library

description: Transmission electron micrograph of a rat type II cell, after inhalation of 300 ppm ethoxyethane, but pretty normal looking.
description: Gender: male
Subspecies: Long evans hooded
Tissue: periperhal
Voltage: 60kv
Stain 1: 1% omium tetroxide
Stain 2: lead citrate and uranyl acetate
Embed: EPON 812
Section: 50-100
description: Preparation: Modified Karnovskys
Item type: pseudocolored transmission electron micrograph
Imaging mode: transmission electron microscopy (TEM)
DOI: 10.4121/0876521b-5bf2-447a-bdad-2369352b917b.v1
title: Data accompanying Chapter 3 of the thesis: Enabling ship changeability; a lifecycle approach to the maritime energy transition

description: This collection contains datasets created as part of the doctoral thesis "Enabling ship changeability; a lifecycle approach to the maritime energy transition by Jesper Jan Zwaginga, M. Sc in Delft University of Technology, 2020-2025.<br>It is being made public both as supplementary data for the thesis and for other researchers to use in their own work.<br>The data is part of the project READINESS, project number TWM.BL.019.002, of the research programme“Topsector Water & Maritime: the Blue route,” which is partly financed by the Dutch Research Council (NWO).<br>The dataset included in this repository consists of several zip files that contain relevant data for each method application from chapter 3:1. Chapter 3.1 Exploratory methods: contains data to reproduce figures for the RDM, RSC and DAPP method investigation2. Chapter 3.2 Search methods: contains data to reproduce figures for the SP and ARO method investigation
DOI: 10.6075/j0x9293r
title: CIL:50601, Homo sapiens, monocyte. In Cell Image Library

description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: Imaging mode: microscopy
Visualization methods: x100
description: The monocyte type cell contained one erythrocyte.
DOI: 10.6075/j0w66jdv
title: CIL:50519, ultrastructural features in AD neurons. In Cell Image Library

description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer‚Äôs disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope. Stereo viewing and computer assisted serial reconstruction techniques were employed to visualize three-dimensional relationships among cytoplasmic components of cortical neurons.
description: We observed several interesting ultrastructural features in AD neurons. These include associations of paired helical filaments (PHF) with the membranes of the nuclear envelope and with ribosomes, differences between the distribution of the Golgi apparatus in neurons containing paired helical filament bundles as compared to neurons without these filaments, and abnormalities in the microtubules of neuronal processes in the vicinity of neuritic plaques.
description: Item type: recorded image
Imaging mode: serial section TEM
DOI: 10.6075/j0fb51kv
title: CIL:50512, cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer's disease. In Cell Image Library

description: We observed several interesting ultrastructural features in AD neurons. These include associations of paired helical filaments (PHF) with the membranes of the nuclear envelope and with ribosomes, differences between the distribution of the Golgi apparatus in neurons containing paired helical filament bundles as compared to neurons without these filaments, and abnormalities in the microtubules of neuronal processes in the vicinity of neuritic plaques.
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer‚Äôs disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope. Stereo viewing and computer assisted serial reconstruction techniques were employed to visualize three-dimensional relationships among cytoplasmic components of cortical neurons.
description: Item type: recorded image
Imaging mode: serial section TEM
DOI: 10.6075/j0np2324
title: CIL:50453, Mus musculus, Mouse brain tissue. In Cell Image Library

description: Brief description of sample preparation
After cryofixation by high-pressure freezing and freeze-substitution, cryofixedmouse brain slices were rehydrated gradually. Rehydrated samples were then imaged with confocal microscopy to capture the DRAQ5 and tdTomato signals. Next, the samples were stained using a high-contrast en bloc staining protocol. Then the samples were dehydrated for resin infiltration and embedding, followed by imaging with X-ray microscopy and then SBEM.

Confocal Microscopy
After freeze-substitution and rehydration, the mouse brain slice was placed in ice-cold 0.15 M sodium cacodylate for imaging. Confocal volumes of DRAQ5 and tdTomato signals were collected on an Olympus FluoView 1000 confocal microscope with a 20X air and 60X water objectives using 561 nm and 633 nm excitation.
description: Item type: recorded image
Imaging mode: confocal microscopy
description: In this study, we developed an electron microscopy method, called CryoChem, to optimally preserve the morphology of genetically labeled tissues. This method also allows us to perform 3D correlated light and electron microscopy (CLEM) in the well-preserved tissue. This dataset contains the tdTomato confocal volume of the CLEM experiment in a mouse brain expressing tdTomato in corticotropin releasing factor-expressing neurons.
DOI: 10.6075/j0m32t9s
title: CIL:49169, Homo sapiens. In Cell Image Library

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.
description: Plate 24638 - 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.
DOI: 10.6075/j0nv9gtx
title: CIL:49168, Homo sapiens. In Cell Image Library

description: Plate 24639 - 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: 10.6075/j0br8qq8
title: CIL:49167, Homo sapiens. In Cell Image Library

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.
description: Plate 24640 - 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.
DOI: 10.6075/j02r3qz1
title: CIL:40280, Ipomea purpurea, pollen. In Cell Image Library

description: Preparation: acetolysis
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: gold
Processing history: unprocessed raw data
description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
description: Scanning electron micrograph of Ipomea purpurea (Morning Glory) pollen. These specimens have been acetolyzed to remove cytoplasm and pollenkit in order to reveal the intricate wall structure. This is part of a large image collection of scanning electron micrographs of pollen samples. Images of a particular species are grouped together. However, to find images and groups of images from other species, please search for the the name of the contributor, Louisa Howard.
DOI: 10.34810/data1950
title: Synthetic datasets of UNICO 5G TIMING project

description: This data set complies datasets generated with simulated data generated in the framework of UNICO 5G TIMING project.
DOI: 10.6075/j0fn15jn
title: CIL:39114, 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; unprocessed raw data
Data qualification: Raw
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol, and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: A view of the cytopharynx and its nascent food vacuole forming region. The flattened pharyngeal vesicles that may contain monolayers or bilayers of lipids seem to be equivalent to the discoidal vesicles of Paramecium that provide membrane for food vacuole growth. They approach and fuse with the cytopharyngeal membrane between the lamellae (cytopharyngeal ribbons). TEM taken on 7/29/67 by R. Allen with Philips 200 operating at 60kV. Neg. 9,000X.
DOI: 10.6075/j0q23z1t
title: CIL:13600, Mus musculus, skeletal muscle cell. In Cell Image Library

description: TA muscles were isolated by dissection, frozen in liquid nitrogen–cooled 2-methylbutane, and embedded in TBS tissue freezing medium. Sections of 10-μm thickness were made with a cryostat at -20°C, placed on uncoated slides, and stained with hematoxylin and eosin. The stained slides were examined with a microscope (DMI 4000B), and the images were captured with a Fluotar 20× 0.4 NA dry objective (Leica) using a camera (RETIGA Exi). The images were processed as 24-bit colored images using Photoshop.
description: Preparation: cryostat-sectioned tissue; Fix in liquid nitrogen–cooled 2-methylbutane
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain; compartmentalization of stain or label
Visualization methods: hematoxylin; eosin
Processing history: Brightness and Contrast Adjusted
Data qualification: Processed;spatialmeasurements
description: Mouse hind limb tibialis anterior (TA) muscles were injected with BaCl2 followed by daily systemic administration of rapamycin (Rap) starting 7 days after injury. The animals were sacrificed at different days, and the injured muscles were dissected and cryosectioned followed by hematoxylin (blue) and eosin (pink to red) staining.

This image shows the regeneration of muscle tissue fourteen days after the injury with daily systemic administration of Rap and trichostatin A (TSA) from day 7 to day 13. The growth inhibition of myofibers by Rap was rescued by TSA. Myofibers were stained by eosin in red and nuclei were stained by hematoxylin in blue. This image corresponds to Fig 10B from JCB 189: 1157-1169, 2010. See also CIL: 13595, 13596, 13597, 13598, and 13599.
DOI: 10.6075/j00p0zpw
title: CIL: 53684, Homo sapiens, HeLa. In Cell Image Library

description: CMGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy