cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0j38rvs
title: CIL:2210, Caenorhabditis elegans. In Cell Image Library

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
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 4 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/j0mw2gfc
title: CIL:221, Homo sapiens, erythrocyte. In Cell Image Library

description: Red blood cells (erythrocytes). This image of human red blood cells obtained by scanning electron microscopy, revealing their characteristic biconcave shape.
description: The scanning electron microscope scans the specimen with a finely focused electron beam and records the number of electrons emitted at each point in the scan as a grey level in the image, with low levels corresponding to few emitted electrons and high levels corresponding to many emitted. Specimens are usually coated with a thin layer of metal to improve conductivity and increase the efficiency of secondary electron emission.
description: Preparation: critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: secondary electron generation; elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0xk8dvw
title: CIL:2209, 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 4 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/j04q7t9j
title: CIL:2207, Caenorhabditis elegans. In Cell Image Library

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 4 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: 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/j089155q
title: CIL:2205, 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 4 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: 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.
DOI: 10.6075/j0cf9q47
title: CIL:32095, Homo sapiens, osteocarcenoma. In Cell Image Library

description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
DOI: 10.15468/dl.rfa4uj
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "GadmGid is COL.28_2",
 "Geometry POLYGON((-151.23345 -32.52691,11.23345 -32.52691,11.23345 32.52691,-151.23345 32.52691,-151.23345 -32.52691))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Diplazium grandifolium"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009295-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0dn4560
title: CIL:39972, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Single transmitted light section from a through focus series through a photoconverted medium spiny cell from the neostriatum of a wild type mouse. Flocculent material surrounding the labeled cell is likely photoconverted mitochondria or non-specific debris produced by the photoconversion procedure. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database, where the reconstruction of the entire cell can also be found.
description: Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Visualization methods: intracellular filling
Data qualification: Processed
description: Tissue was prepared from a 7 month adult male mouse strain, C57BL/129SvJ. Tissue sections, 100µm, were generated using a vibratome. The entire through series of images were gathered using a Bio-Rad Radiance 2000 with a Nikon Plan Apo 60X 1.4 NA.
DOI: 10.6075/j0bz64m6
title: CIL:46287, 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 25739 - 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/j0vx0fmz
title: CIL:13177, Micrasterias denticulata. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
description: Micrograph illustrating the Golgi apparatus and rough endoplasmic reticulum (RER) cell stabilized by ultrarapid freezing. Note the relationship of the RER membrane to the Golgi complex. 

Technical details:
Cultures of Micrasterias denticulata were obtained from the Algal Culture Collection, University of Indiana (Cat. No . LB558) . Cells were grown in Waris medium MS at 18°C on a 15/9-h, fight-dark cycle. For each experiment, cells about halfway through the dark cycle were placed in fresh medium in continuous light. This treatment stimulated many cells to divide ~25 h later. Healthy, growing cells were then selected with a dissecting microscope and placed in a separate Petri dish containing growth medium buffered with 2 mM 2(N-morpholino)-ethane sulfonic acid adjusted to pH 6.0. Cells at the desired stage of development were then placed in another dish containing 1% glutaraldehyde in buffered medium and fixed for 20 min. Gold double-replica supports (Balzers High Vacuum Corp ., Santa Ana, Calif.) were coated with a thin layer of yeast paste. Fixed cells were placed on one support and the second support was placed on top. This "sandwich" was plunged into liquid propane near its melting point and stored in liquid nitrogen. Cells were ultrarapidly frozen using a propane-jet device of the type described by Miiller et al (see reference). Samples were prepared as described above, with the following exceptions: cells were frozen directly in growth medium, without prior fixation; the gold supports used had been hollowed out, leaving a metal thickness of 127 micron and the propane-jet device was used. Samples were fractured and replicated using a Balzers double-replica device in a Balzers BA 360 freeze-etch unit. Fracturing was done at -110°C. The yeast paste allowed recovery of large, intact replicas; these were cleaned in commercial bleach and 70% sulfuric acid at 60°C. Replicas were examined in a JEOL EM 100C at 26,000X magnification.

Image reference: PMID: 7364870.
Ribosome binding sites visualized on freeze-fractured membranes of the rough endoplasmic reticulum. Giddings TH Jr, Staehelin LA. J Cell Biol. 1980 Apr;85(1):147-52.
DOI: 10.6075/j0ng4pdb
title: CIL:25359, Canis lupus familiaris, epithelial cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: monolayer
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: Reorganization of cells around a site of cell extrusion monitored live by time-lapse differential interference contrast microscopy. The process of extrusion began at hour 1 of observation and continued for 40 min. Monolayer was imaged on a Zeiss Axiovert 200M microscope using a 40× dry differential interference contrast microscopy (DIC) objective. Images were collected by a charge-coupled device camera (CoolSNAP-HQ, Photometrics, Tucson, AZ) and stored digitally every 10 min. Image corresponds to Fig 4 and Video 1 in PLoS Pathog. 2006 Jan;2(1):e3. Epub 2006 Jan 27.
DOI: 10.6075/j0z31xfj
title: CIL:24792. In Cell Image Library

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).
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: Electron micrograph of keratocyte or fibroblast lamellipodial actin network after latrunculin a (a chemical that binds monomeric actin) treatment (0.2 μM for 10 min). All examples demonstrate frequent branching of actin filaments. Image corresponds to Figure 2c in J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6075/j0m044sh
title: CIL:40697, Mus musculus, fibroblast. In Cell Image Library

description: Chromosomes were isolated from metaphase cells using a non-aqueous protocol, exposed to non-ionic detergent for 2 hr, fixed with formaldehyde, deposited on a carbon-coated grid,stained with uranyl acetate, and critical point dried.
See also:
H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: isolated subcellular component
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High voltage (1MeV) transmission electron microscopy image of an isolated metaphase chromatid pair from a mouse A9 cell, showing the fibrous structure. The image was taken with a specimen tilt of 53 degrees. Grouped with it is an image with a tilt of 45 degrees, providing a pair that affords an oblique stereo view of the chromosome.
DOI: 10.6075/j0c24v7j
title: CIL:38976, Homo sapiens, embryonic gland hemocyte. In Cell Image Library

description: Preparation: chemically fixed tissue
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: visualization of contiguous regions
Processing history: colorized
description: Scanning electron micrograph of a 6 day old human embryo beginning to implant into the lining of the uterus (endometrium). As implantation progresses, the inner cell mass begins to form into the bilaminar disc. The two layers are called the epiblast and the hypoblast. An embryo that has been in culture for up to 14 days will remain at this stage of development. Such cultured embryos remain alive but do not progress as they would in the womb.
description: B0003308 6 day old human embryo implanting. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0d799b6
title: CIL:39008, retinal neuron. In Cell Image Library

description: This fluorescent micrograph shows a microelectrode penetrating the cell body of a neurone in the retina of a living eye. The electrode is injecting a fluorescent dye (lucifer yellow) into the cell, filling its branch-like dendrites which form connections with other nerve cells.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: lucifer yellow
Processing history: unprocessed raw data
description: B0000061 Injection of retinal cell Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0qf8sbg
title: CIL: 51769, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0dv1j9t
title: CIL: 50934, Human mast cell line (HMC-1), Human mast cells. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Human mast cell line 1 (HMC-1) were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
DOI: 10.6075/j0hx1b8h
title: CIL:47672, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - CDB18 A4 block)