cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0jm28jv
title: CIL:39108, epithelial cell of lung. In Cell Image Library

description: Relation to intact cell: dispersed cells in vitro
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: visualization of contiguous regions
Processing history: colorized
description: B0007209 Lung cancer cell. Wellcome Image Award Winner 2009. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: This scanning electron micrograph shows a single cell grown from a culture of lung epithelial carcinoma cells. The purple area shows blebs, which are irregular bulges in the plasma membrane of the cell caused by localized decoupling of the cytoskeleton from the plasma membrane. The green area shows an area of the cell where the blebbing is not occurring or is not visible.
DOI: 10.6075/j0n29vkd
title: CIL:28757. In Cell Image Library

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.30 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j03b5xx0
title: CIL:40428, Saccharomyces cerevisiae, vma9 mutant. In Cell Image Library

description: Transmission electron micrograph of a concentric multilamellar body from a sertraline-treated vma9 mutant cell. (40,000X). This is part of an image group highlighting multilamellar structure, CIL: 40428-40430.
description: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j00r9n3n
title: CIL:13715, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: EYFP; probe for mitochondria; CMX rosamine (Mitotracker Red)
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: PINK1-YFP R98F (green) is found localized to mitochondria (red) in the absence of the mitochondrial depolarizing agent CCCP (carbonyl cyanide-m-chlorophenyl hydrazone). The R98F mutation in PINK1-YFP partially inhibits proteolytic cleavage. HeLa cells expressing PINK1-YFP R98F were stained with 10nM MitoTracker Red for 30 min to see mitochondrial morphology and then treated with DMSO for 3 hours. Cells were imaged using an inverted microscope (LSM510 Meta; Carl Zeiss, Inc.) with a 63× 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the accompanying image browser (LSM; Carl Zeiss, Inc.). This image corresponds to Fig 3d, R98F/DMSO bottom panels in J Cell Biol. 191: 933-942, 2010. Images in Fig3d include CIL#s 13713, 13714, 13715, 13716.
DOI: 10.6075/j0hd7tv1
title: CIL:10421, Gallus gallus, erythrocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM); darkfield illumination
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Nucleated erythrocytes from chicken were spread on water, the dispersed chromatin picked up on carbon-formvar grids, fixed with paraformaldehye, critical point dried and shadowed with platinum. Images were obtained with the Wisconsin high voltage TEM at 1MEV using darkfield illumination. For this micrograph, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees providing a stereo pair with an oblique 3D view of the tangled and irregular chromatin fibers is grouped with this image.
DOI: 10.6075/j0g15zgw
title: CIL:37117, Cavia porcellus, pancreas cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); electron microscope autoradiograph
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; metabolically incorporated radioisotope
Processing history: unprocessed raw data
description: Anesthetized animals were intravenously injected with 1-5 millicuris of DL-leucine 4,5-H^3 with a specific activity of 3570 mc/mM. At times ranging from 4 min to 15 hrs after injection the pancreas was removed and fixed in osmium tetroxide. Tissue was embedded in methacrylate, sectioned, and post-stained with uranyl acetate. 

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x10,000.
description: Electron microscope autoradiograph showing radioactivity associated with zymogen granules in the guinea pig pancreas 4 hrs after injection. Image corresponds to Figure 9 in J Cell Biol. 1964 Mar;20:473-95. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0x63m48
title: CIL:10722, Notophthalmus viridescens, oocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Meiotic newt oocyte nuclei were allowed to disperse in 30 mM KCl/NaCl, centrifuged through 2% formaldehyde onto an EM grid, stained with uranyl acetate, and critical point dried. Grids were examined with the Madison 1MeV TEM at 10 KX. This micrograph, showing transcription on looped lampbrush chromosomes was recorded at a tilt angle of 45 degrees. The image is grouped with one of the same sample area recorded at a 55 degree tilt. A stereo examination of the pair provides an oblique 3D view.
DOI: 10.6075/j0k072x9
title: CIL:34899. In Cell Image Library

description: Improved visualization of actin filament branching in lamellipodia. EM of keratocyte or fibroblast lamellipodial actin network after cytochalasin D treatment (0.2 μM for 30 min or 0.5 μM for 10 min). Image corresponds to a panel in Figure 2b from J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 2b are available as CIL 34894-34901.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: shadowing and plating; platinum replica
Processing history: unprocessed raw data
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
DOI: 10.6075/j04b305h
title: CIL:40997, Rattus rattus, reticulocyte. In Cell Image Library

description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi.
description: Preparation: chemically fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Data qualification: Processed
description: Transmission electron micrograph of a thin section of a capillary from the ventricular myocardium of the rat showing part of a reticulocyte (immature erythrocyte) in the lumen of the capillary. The reticulocyte cytoplasm is devoid of membranous organelles but contains free polyribosomes (also known as polysomes) which primarily synthesize globin during the late stages of erythrocyte maturation.
DOI: 10.6075/j0td9x3z
title: CIL: 54002, Homo sapiens, HeLa. In Cell Image Library

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: STE 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: Visualization methods: confocal microscopy
DOI: 10.6075/j05x27hp
title: CIL:46053, 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 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.
description: Plate 26641 - 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.
DOI: 10.6075/j0pk0gh1
title: CIL:57280. In Cell Image Library

description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j04m94x2
title: CIL:57384. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
DOI: 10.6075/j0cz37h8
title: CIL:57325. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j03n23rs
title: CIL:57248. In Cell Image Library

description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j0c53m6v
title: CIL:57385. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j00v8d59
title: CIL:57379. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.15468/dl.27xvr2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Toombatrachia"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009664-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0rb74zk
title: CIL:57388. In Cell Image Library

description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j0w37wpx
title: CIL:57387. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j01v5fb4
title: CIL:57338. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
DOI: 10.6075/j0tb1786
title: CIL:57296. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.5281/zenodo.15179825
title: Interfacial engineering of conformal titanium oxide nanofilms on porous carbon supercapacitor electrodes via atomic layer deposition

description: The growth mechanism of titanium dioxide onto activated carbon was determined through the growth per cycle values. The crystal structure of the deposited films was determined using x-ray diffraction and the surface defect sites of the samples are measured by Raman spectroscopy. X-ray photoelectron spectroscopy was utilized to confirm the presence of titanium dioxide and it associated surface functional groups. Surface morphology and elemental composition studies were utilized to analyze the film uniformity and a high resolution cross-sectional images to study the film conformity. Extensive charge-discharge cycles were performed to calculate the specific capacitance and the equivalent series resistance. Cyclic voltammetry studies were utilized to study the electrochemical behavior of the bare and titanium dioxide coated activated carbon electrodes.
DOI: 10.6075/j0d21xzz
title: CIL:57331. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j0mk6d78
title: CIL:57382. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
DOI: 10.6075/j0nk3fcn
title: CIL:57335. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Ebola virus Huh7 infected cells 22 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j06h4hsh
title: CIL:57286. In Cell Image Library

description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
DOI: 10.6075/j02v2gf2
title: CIL:57284. In Cell Image Library

description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.
description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
DOI: 10.6075/j0b858gs
title: CIL:57292. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM); thin-section
description: Pixel size: 8.25 Å ; image size: 2048x2048; Samples were chemically fixed, high-pressure frozen and freeze substituted in HM20, thin sections 100 nm thickness.
description: Ebola virus Huh7 infected cells 18 hours post infection, anti-nucleocapsid immuno-golg labelling.