cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0348jgp
title: CIL:12023, Nephrotoma, Nephrotoma suturalis, primary spermatocyte. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: differential interference contrast microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: differences in refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Movie of meiosis I (diakinesis through telophase)in primary spermatocytes of the crane-fly Nephrotoma suturalis that have been experimentally flattened. Flattening prevents completion of cytokinesis.
Time-lapse DIC microscopy using a Nikon 
Microphot SA, equipped for liquid crystal polarized light microscopy 
(LC-PolScope, CRi, Woburn Massachusetts) 60x/1.4 PlanApo oil immersion objective, 1.4 NA oil imm. condenser, with 2.0x zoom lens. Images captured every 2 min for 179 min using a QImaging Retigo EXi CCD camera. The time series on which the movie is based is included in this grouped set.
DOI: 10.6075/j06972s6
title: CIL:1131, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. 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: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
DOI: 10.6075/j0pn95q3
title: CIL:12554, Rattus, multipolar neuron. In Cell Image Library

description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0g73cfq
title: CIL:13905, Caenorhabditis elegans, embryo. In Cell Image Library

description: Representative image indicative of autophagic activity of C. elegans (WT; N2 Bristol isolate) embryo expressing a full-length plgg-1DsRED::LGG-1 fusion fed with UV-killed Escherichia coli without additional 0.2mM spermidine. Epifluorescence microscopy was performed with a microscope (AxioImager Z2; Carl Zeiss, Inc.) using a Plan Neofluar 40× objective with a 0.75 NA and a 63× Plan Neofluar objective with an NA of 1.25 in oil at RT using a 540 ± 15–nm band-pass excitation filter and a 575-nm long-pass emission filter. Images were taken with a camera (AxioCam MRc5; Carl Zeiss, Inc.) with Axiovision software (Carl Zeiss, Inc.) without further processing. Image: Figure 3A, top left panel, in Morselli et al. J Cell Biol 192: 615-629
description: Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: DsRed
Data qualification: Raw;intensitiesquantitation
DOI: 10.6075/j0v9875g
title: CIL:10519, Toxoplasma gondii RH. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Data qualification: Raw;spatialmeasurements
description: DIC z-series of extracellular Toxoplasma gondii. T. gondii tachyzoites (strain RH) were cultivated in human foreskin fibroblast cells and parasites were harvested soon after emerging from host cells. Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 60X water immersion, 1.2 NA. Captured with CoolSnapHQ/ICX285.

Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.13140/rg.2.2.16092.60804
title: 3D Reconstruction. Design patent RU 138877
DOI: 10.6075/j0057dzb
title: CIL:2742, 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 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: 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: 10.5281/zenodo.17491046
title: Global Ocean Physics Reanalysis

description: daily and monthly mean files for temperature, salinity, currents, sea level, mixed layer depth and ice parameters from the top to the bottom of the ocean

For more details, check the primary source here
DOI: 10.6075/j0dj5d5s
title: CIL:49158, Homo sapiens. In Cell Image Library

description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery. Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities. The experiment consists of 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

The experiment consists of 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
description: Plate 24654 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules. The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the cell-painting assay). This experiment consists of 375 plates in 384-well format, for a data set comprised of 988,994 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are approximately 5 million image files in 16-bit TIFF format.
DOI: 10.5281/zenodo.17491045
title: Global Ocean Physics Reanalysis

description: daily and monthly mean files for temperature, salinity, currents, sea level, mixed layer depth and ice parameters from the top to the bottom of the ocean

For more details, check the primary source here
DOI: 10.6075/j0cv4hvd
title: CIL:40223, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

description: Detailed methods can be found at the CCDB link provided. Briefly, one month old male mouse (C57BL/6NHsd) was perfused with Ringer's solution for 2 minutes followed by 2% glutaraldehyde and 2% paraformaldehyde in 0.15M sodium cacodylate buffer, pH 7.4. Further dissection of tissue was followed with postfixation using 1% OsO4, additional staining using 2% uranyl acetate, processed for embedding in durcupan ACM resin, and sectioned at a thickness of 5µm thick. Serial tomograms were produced from single tilt images using a JEOL4000, with 8k x 8k CCD camera, 5000X, 400.0 keV).
description: Single computed slice through a tomographic reconstruction of the cell body of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. The reconstruction is the 6th in a series of 26 serial reconstructions through the cell soma. All 26 images can be found in this image group within the Cell Library, and the complete reconstruction can be viewed in the Cell centered database, accession # 7503.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt
Data qualification: Processed
DOI: 10.6075/j0wq02tb
title: CIL:2721, 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 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: 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/j0h70f8g
title: CIL: 51701, 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: 10.13140/rg.2.2.29514.38086
title: 3D Reconstruction. Design patent RU 138962
DOI: 10.6075/j0c24v46
title: CIL:13587, Mus musculus, myoblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: The image was taken by leica DMI 4000B microscope equipped with a QImaging RETIGA Exi camera and Leica 10X/0.22 lens. 

Myosin heavy chain (MHC) expressed in myotubes was labeled by MF-20 mouse antibody followed by FITC-anti-mouse IgG secondary antibody. Nuclei were stained by DAPI. MHC and nuclei were pseudocolored in green and blue, respectively.
description: The C2C12 cell line, a mouse myoblast line, was used here to study the regulatory factors in myogenic differentiation. After cultured in differentiation medium for 3 days, these cells differentiated into myotubes (Green) containing multiple nuclei (Blue). The myoblasts in this image were transfected with the locked nucleic acid (LNA) anti-miR-1 and treated with 25 nM trichostatin A (TSA), an inhibitor of histone deacetylase (HDAC), the day before switching to differentiation medium. The effect of miR-1was rescued by TSA.

This image is one of different treatments in Figure 6B from JCB 189: 1157-1169, 2010. See also CIL: 13585, 13586, 13588.
DOI: 10.6075/j09w0d79
title: CIL:13560, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: An ER-trapped GalNac-T activity reporter (Muc-PTS; fused to GFP) (green) is targeted to the ER and not the Golgi, marked by Giantin (red) in HeLa cells cotransfected with inactive Src (SrcK-mCherry, containing K295M mutation) (gray). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa 647 for anti-Giantin and Hoechst (blue). Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 5C in J Cell Biol. 189: 843-858. 2010. Images in Fig 5 include CIL#s 13559, 13560, 13561, 13562.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; EGFP; mCherryFP; primary antibody plus labeled secondary antibody; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0t72g4n
title: CIL:13562, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: An ER-trapped GalNac-T activity reporter (Muc-PTS; fused to GFP) (green) is targeted to the ER marked by PDI (protein disulfide isomerase) (red) in HeLa cells cotransfected with active Src (SrcE-mCherry, containing E378G mutation) (gray). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa 647 for anti-PDI and Hoechst (blue). Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 5D in J Cell Biol. 189: 843-858. 2010. Images in Fig 5 include CIL#s 13559, 13560, 13561, 13562.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; EGFP; mCherryFP; primary antibody plus labeled secondary antibody; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j02f7m6b
title: CIL:13561, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; EGFP; mCherryFP; primary antibody plus labeled secondary antibody; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: An ER-trapped GalNac-T activity reporter (Muc-PTS; fused to GFP) (green) is targeted to the ER and not the Golgi, marked by Giantin (red) in HeLa cells cotransfected with active Src (SrcE-mCherry, containing E378G mutation) (gray). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa 647 for anti-Giantin and Hoechst (blue). Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 561 nm and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 5E in J Cell Biol. 189: 843-858. 2010. Images in Fig 5 include CIL#s 13559, 13560, 13561, 13562.