cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09k4bb7
title: CIL:39957, Mus musculus, Purkinje cell. In Cell Image Library

description: Tissue was perfused with paraformaldehyde, sectioned (100 µm) on a vibratome and mounted in gelvatol, and imaged on a Biorad Radiance 2000 Confocal using a 60x 1.4NA objective.
description: A Purkinje neuron from the cerebellum of a 2 month old male C57BL/6 mouse, injected with Lucifer Yellow. The elaborate, highly branched dendritic arbor is revealed in this maximum projection image which was generated by compiling a z-series of optical sections. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: 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: 10.15151/esrf-es-2233629579
title: Application of High-Energy-Resolution X-ray Absorption Spectroscopy at the U M edge to Assess U(V) Electronic Structure in U(V) compounds

description: The oxidation state of uranium (U) largely controls its migration behavior in the environment. Recent studies have evidence the
importance of minor chemical
species of U(V), especially when interacting with minerals such as magnetite. Recently, the HERFD-XANES method has been used to detect U
(V) species, but there are a few U(V) compounds used as standard spectra. To establish a more accurate U(V) speciation method,
measurement of other U(V) compounds is indispensable.
We will conduct HERFD-XANES analysis at the U M-edge to clarify the spectral differences between U(V) oxides with different crystal
structures, such as monouranate compounds, isostructural mixed oxides and U adsorbed on Fe-oxides. These results will allow us to clearly
define the U valence and to discuss the difference of electronic structure of U(V) in each compound. Furthermore, the suitable speciation
method for U(V) compounds can be determined by discussing the results in combination with the U L-edge HERFD-XANES.
DOI: 10.6075/j0dz074h
title: CIL:30564, Drosophila melanogaster, early embryonic cell. In Cell Image Library

description: Dynamics of spindle microtubules and chromosomes during cycle 11 in a transgenic Drosophila embryo expressing GFP-tubulin (green) and histone-RFP (red). Only a single confocal plane containing the centrosomes was acquired during imaging. Images were acquired with exposure times of 1.8 s for GFP and 0.6 s for RFP, and total time shown is 432 s. This time series is the original data from Video 1 "Dynamics of spindle MTs and chromosomes during cycle 11 in a transgenic Drosophila embryo expressing GFPtubulin and histone-RFP" from Civelekoglu-Scholey et al.(2010) Prometaphase spindle maintenance by an antagonistic motor-dependent force balance made robust by a disassembling lamin-B envelope, J. Cell Biol. 188(1):49-68.
description: Embryos expressing GFP-tubulin and histone-RFP were collected at 25°C for 1 h, matured for 40 min, dechorionated, placed on heptane glue and covered with halocarbon oil. Images from this image group were acquired with an inverted IX-70 Olympus with Ultra-View spinning disk confocal head (PerkinElmer) and acquired with an oil immersion objective (UPlan-Apochromat 100x N.A. 1.35, or Plan-Apochromat 60x NA 1.4). Time series (at intervals of 3 to 10 sec) z-stacks of planes at 0.5 µm were acquired with an Orca II CCD camera (Hamamatsu Photonics). For further information see J. Cell Biol. 188(1):49-68.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Green fluorescent proteins from Aequorea; mRFP1
Data qualification: Raw
DOI: 10.6075/j0vh5mq4
title: CIL:41457, Nephrotoma suturalis, spermatocyte. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: orientation independent differential interference contrast microscopy
Parameter imaged: optical path length
Source of contrast: regions with different refractive index
description: Nephrotoma suturalis spermatocyte (crane fly sperm cell) during metaphase in meiosis. Image was captured using a newly developed orientation-independent differential interference contrast technique. Judges' Special Award for Technical Merit, 2010 Olympus BioScapes Digital Imaging Competition©. For additional details on the microscopy method see: M.Shribak, J.LaFountain, D.Biggs, S.Inoue, Journal of Biomedical Optics, vol. 13, No.1, 14011 (2008).
DOI: 10.6075/j09g5kcx
title: CIL:45967, Homo sapiens. In Cell Image Library

description: Plate 25966 - 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: 10.15151/esrf-es-2233034632
title: Very Long-Distance MLL Development and in-situ & in-operando Setups for X-ray Nanodiffraction Analysis of Thin Films and Energy Components

description: The project focuses on the development of multilayer Laue lenses (MLLs) for ID13. Previous experiments have already shown focal spot sizes down to ~23 nm with diffraction efficiencies up to about 29 %. The main instrumental goal of this LTP is the development of two types of MLL optics, namely (i) “very long-distance” with a focal length of up to ~150 mm, a working distance of &gt;100 mm (@ 12 keV) and an optics aperture of up to ~ 200 µm × 200 µm and (ii) “a new high resolution” lens pair with a focal spot size down to half of the present value, reaching ~10 nm. The MLLs will be used to perform (i) in-situ micromechanical tests on thin films and fibers using a dedicated indenter and (ii) in-operando electro-chemo-mechanical tests on solid state batteries (SSBs). For this purpose, the indenter from MI-1355 will be further developed by implementing new sample mounts, wedge and flat-punch tips and tensile option. Additionally, an adaptable in-operando cell to test SSBs will be designed.
DOI: 10.15151/esrf-es-2233038911
title: Search for crystallographic signatures of spin-crossover transition in the layered Ruddlesden–Popper-type cobalt oxychlorides Sr2CoO3Cl and

description: We propose to study the pressure effect on structure of the layered Ruddlesden–Popper-type cobalt oxychlorides Sr2CoO3Cl and Sr3Co2O5Cl2. These compounds are antiferromagnets with high Neel temperature TN&gt;300 K. Co(3+) ions in these compounds are square-pyramidally coordinated and thus possess pure high-spin state. Application of high pressure might lead to spin-crossover transition to low-spin state changing the magnetic and electronic properties of material. Co(3+) cation takes the low-spin state being octahedrally coordinated. Thus, the structural evolution under pressure can provide a hint for spin-crossover transition. Combined with electronic transport measurements, Co Kβ X-ray emission spectroscopy and electronic structure calculations obtained results will allow to unravel the interplay between crystal structure and magnetic and electronic properties of Co-based perovskite-like materials.
DOI: 10.6075/j0cn72x0
title: CIL:7110, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j0zp44p5
title: CIL:45974, Homo sapiens. In Cell Image Library

description: Plate 25987 - 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/j01c1vwx
title: CIL:2823, 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: 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.
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/j0db80pm
title: CIL:40561, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Acidosomes originate from the biosynthetic pathway that includes the ER, the Golgi stack and the trans-Golgi network (TGN). Flattened vesicles from the TGN round up into spherical vesicles and bind to microtubules (not shown here) that come from the cytopharynx. While moving along these microtubules they come into contact with the carrier vesicles that also bind to the same microtubules. TEM taken on 7/19/88 by C. Schroeder with Zeiss 10A TEM. Neg. 24,800X. Published in J. Cell Sci. 106:411-422, 1993. Adapted with permission.
description: 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: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0qr4w4m
title: CIL:2554, 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 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.
DOI: 10.6075/j08k780r
title: CIL:25690, Trichodina, Chlorella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A view of the entry to the oral apparatus of the green Trichodina that lives on the surface of a freshwater snail collected in central Illinois. In this view the haplokinety and the polykinety of the oral apparatus is cut transversely and an endosymbiotic zoochlorellae are evident. In the case of the haplokinety, there is a gradual view of cross-sections from the axoneme of the cilium through the transition zone to the upper part of the basal body. The haplokinety is distinguished by a single row of ciliated basal bodies and the adjacent outer polykinety is composed of three rows of ciliated basal bodies. The cortical underpinning of the oral cortex is evident. TEM taken by G. Antipa in 1968 with a Hitachi HU11A operating at 75kV. The negative magnification is 7,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 65nm thickness.
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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0639nsx
title: CIL:2558, 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: 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/j0mw2g5s
title: CIL:2557, 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: 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: 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/j0ft8k35
title: CIL:2559, 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 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.