cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17490889
title: Peer Pings and Self-Control: WhatsApp Group Norms, Short- Video Algorithms, and Risky Adolescent Behaviour in Indonesia

description: This dataset comprises survey and trace-based measures from 1024 Indonesian secondary students nested within 52 classes across 18 schools, including multi-item scales of self-control, WhatsApp-based peer injunctive and descriptive norms, and risky online/offline behaviors, alongside smartphone-derived notification density and detailed short-video platform usage (TikTok/Reels/Shorts, autoplay status, and algorithmic-feed share). Variables are organized for multilevel analysis (student/class), with item-level Likert responses and constructed indices (e.g., algorithmic exposure composite), enabling CFA and MSEM to examine how peer norms, self-control, and algorithmic curation jointly predict adolescent risk outcomes.
DOI: 10.6075/j0fq9vxk
title: CIL:1966, 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/j05h7fvd
title: CIL: 52966, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Image 4, z=17 from SC_011
DOI: 10.6075/j05m64j9
title: CIL:11193, Rattus, Ovis aries, Sertoli cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed
description: Occluding junctions in Sertoli cells of ram and rat testis. Multiple focal sites of membrane fusion are indicated by arrows in each panel. Underlying these sites, associated bundles of filaments and typical subsurface cisternae are apparent in panels A, B and D. A, B, C from Gilula, Fawcett and Aoki, Dev. Biol. 50: 142068, 1976; D, Dym and Fawcett, Biol. Reprod. 3: 308-26, 1970; Inset from Wade and Karnovsky, J. Cell Biol., 60:168-91 illustrates two models regarding the relationship between the two cell membranes at these junctions. Regions indicated by asterisks in the micrograph in panel C support model "A." Micrographs reprinted with permission as Figure 69 from Chapter 3 (Junctional Specializations) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0vm4bv8
title: CIL: 53068, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Image 4, z=14 from SC_028
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0833rgg
title: CIL: 51293, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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.
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.
DOI: 10.6075/j0zp457r
title: CIL:9852, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: The contractile vacuole pore is encircled on its cytosolic surface with microtubules. Other microtubules arise from these encircling microtubules and extend far out into the cell where they provide structural support for the several radial arms of the CVC. This CV was in very late systole or very early diastole. b-tubulin is immunogold labeled. TEM taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 9,780X. Bar = 0.5µm. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:38683) is in the library and available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j00z72gv
title: CIL:9719, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The monokinetids (single somatic basal bodies) of Coleps hirtus bear an anteriorly directed striated fibrous kinetodesmal fiber and a posteriorly directed ribbon of postciliary microtubules that arise from the posterior side of each basal body. Both pass to the same side of the row of basal bodies. Transverse microtubules arise from the anterior side of the basal body and pass to the other side of the row of basal bodies. These structures presumably give support to the twisting movements of the beating cilium. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections were prepared at approximately 75nm thickness. TEM taken on 5/23/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. The negative was printed to paper and the image was scanned with a flatbed scanner and 0.5µm bar added in Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:9015) is in the library and available for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0js9psb
title: CIL:40114, Drosophila melanogaster, embryonic cell. In Cell Image Library

description: Preparation: acetone fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: Electron micrograph of a cultured Drosophila DL1 cell infected with flock house virus, prepared by high pressure freezing followed by freeze substitution. This cell was prepared as part of an experiment to investigate different protocols for high pressure freezing. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Cell pellets were directly placed into brass planchettes that then were loaded in to the HPM 010 high pressure freezer and fast frozen.

Freeze substitution: After freezing, samples (2) and (3) were placed into a Leica EM AFS Freeze substitution (FS) machine (Leica Microsystems, Bannockburn, IL) and incubated at -90 deg C for 24 hours in 0.1 percent tannic acid in acetone. Samples were washed three times with cold acetone (cooled to -90 degrees C) over 5 minutes, and placed in 1 percent OsO4 and 0.1% UA in cold acetone for 72 hours and held at -90 degrees C. After slowly warming to room temperature at 5 degrees C per hour, the specimens were rinsed in pure acetone three times (10 min. at room temperature). Infiltration and embedding in Durcupan resin was subsequently performed at room temperature. Images were acquired using a JEOL4000EX IVEM, magnification: 30000.0; accelerating voltage: 80.0 keV.
DOI: 10.6075/j0zc826g
title: CIL:40321, 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: 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.
description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
DOI: 10.6075/j0rf5stx
title: CIL:39709, Saccharomyces cerevisiae, BY4716. In Cell Image Library

description: Transmission electron micrograph of a yeast cell treated with 60¬µM sertraline. This is a high-magnification zoom of CIL 39708 showing a double-membrane autophagosome. A cresecent-shaped lipid droplet is visible, as well as multiple vesicular structures. The image contributor asks Library users to use the comments box to answer the question, what are the electron dense deposits on the surface of the lipid droplet?
description: BY4716 is an auxotrophic haploid laboratory strain of the budding yeast Saccharomyces cerevisiae. Its genotype is lys2Δ, mating type alpha and it is derived from S288c. Sections were embedded in LR white resin, mounted on carbon-coated nickel grids and imaged with LEO 912AB at 80kV and 6,300X. All cells in this batch were grown in liquid rich media (YPD pH6.5) at 30˚C with aerated shaking, and cultures were sampled in mid-logarithmic phase. This image is part of a group of untreated cells and cells 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/j0jw8d8z
title: CIL:38901, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Stacks of 4 or 5 kinetodesmal fibers occupy the longitudinal ridges in a cross-sectioned cell. The kds lie along the right side of each ridge (cell‚Äôs left side), and as the kds are tapered, the smallest cross sections lie closest to the ridge tip and these sections are also closest to the distal tips of the kds. Such a kd arose from basal bodies 4 or 5 cortical units posterior to the plane of the cross-section. Lateral ridges do not contain kds. TEM taken on 12/28/74 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 17,500X.
DOI: 10.6075/j06t0m8m
title: CIL: 53349, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: 17.2 degrees ℃
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 17.2 degrees Celcius
DOI: 10.6075/j01v5dc5
title: CIL:45863, 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 25569 - 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/j0x34wtw
title: CIL:39345, Helianthus annuus. In Cell Image Library

description: Instrument: FEI XL-30 FEG ESEM. Technical protocol available at http://remf.dartmouth.edu:8080/EM-Wiki/36
description: Scanning electron microscope image of sunflower lower leaf surface. Note the numerous stomata, which are pores used for gas exchange. A larger magnification view of a single stomata can be found in CIL 39343. This is part of an image series containing images CIL:39341-39343, and 39345.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde 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: uranyl salt; shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0h993v2
title: CIL:37246. In Cell Image Library

description: Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
description: Stain penetration in remounted thin section. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi.
DOI: 10.6075/j09k49bt
title: CIL:9175, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Sialyl Transferase-EGFP transfected HeLa cells demonstrating the redistribution of the Golgi Apparatus to the Endoplasmic Reticulum upon treatment with Brefeldin A (BFA). 
Images were collected as a 4D time series (z-stack over time). z-stacks of 48 individual timepoints are included in this collection of files as well as the movie SiEGFP_BFA.avi, which is the maximum projection of the z-stacks at the individual time points.

BFA was added according to the following protocol:
Timepoint1: Before addition of BFA 0seconds (8 Z-slices at 1 um apart)
Timepoint2: After addition of BFA 130seconds (8 Z-slices at 1 um apart) 
Timepoint3: 238 seconds (11 Z-slices at 1 um apart) 
Timepoint3 thru Timepoint48: Images captured every 5 seconds (11 Z-slices at 1 um apart at each time point) 

Images were collected on a Carl Zeiss spinning disk confocal with a 63X 1.4 NA objective with 250 ms exposures at 5 s intervals.
description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j00g3htc
title: CIL:34909. 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: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol 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: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data