cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j06w997j
title: CIL:17892, Didinium nasutum, Paramecium sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: chemically fixed tissue; lyophilized specimen; Parducz fixative; Au/Pd metal sputter-coat
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: illumination by electrons; secondary_electron imaging
Parameter imaged: illumination by electrons; secondary electron generation; secondary_electron imaging
Source of contrast: detection of electrons
Visualization methods: shadowing and plating
Processing history: recorded image; film
Data qualification: Raw
description: Didinium ingests Paramecium. Also showing a few discharged trichocysts and metachronous waves of cilia in the two characteristic ciliary girdles of Didinium nasutum. This micrograph was taken in 1968 by G. Antipa on a Cambridge Mark IIA operating at 20kV. The negative magnification is 410X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available for quantitative analysis. Further details are available at Wessenberg, H. and Antipa, G. 1970. Capture and ingestion of Paramecium by Didinium nasutum. J. Protozool. 17:250-270.
DOI: 10.6075/j01835pp
title: CIL:17893, uncultured scuticociliate, Conchophthirus curtus, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: shadowing and plating; chemically fixed tissue; lyophilized specimen; Parducz fixative; Au/Pd metal sputter-coat
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: illumination by electrons; secondary_electron imaging
Parameter imaged: illumination by electrons; secondary electron generation; secondary_electron imaging
Source of contrast: detection of electrons
Visualization methods: Deciliation
Processing history: recorded image; film
Data qualification: Raw
description: Conchophthirus was deciliated by calcium ion shock followed by shearing through a 22 gauge needle. This revealed the location of the deciliated basal bodies and the cell's surface architecture. In this image of the suture line where the left and right side rows of basal bodies converge, one can observe the distribution of the ciliature, and at the suture line the location of the deciliated caudal basal bodies to which 10-20 long caudal cilia are attached. These cilia seem to act as a rudder to help guide the organism as the active beating cilia of locomotor cilia propagate the organism through the media. Also note that, when zoomed in, in this preparation the clathrin coated pits, which are normally an invagination into the cytoplasm have everted following the deciliation procedure, to form a small evagination anterior to the stubb of each deciliated basal body. For more information see: Antipa, G. A. and Small, E. B. 1971. A redescription of Conchophthirus curtus Engelmann, 1862 (Protozoa, Ciliatea). J. Protozool. 18:491-503. This micrograph was taken in 1968 by G. Antipa on a Cambridge Mark IIA operating at 20kV. The negative magnification is 1912X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available for quantitative analysis.
DOI: 10.6075/j0n29wf1
title: CIL: 52293, 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: One z layer of a z-stack at the given tile position
description: Tile x=4, y=1, z=16 from BL_024216_Myc_Terc
DOI: 10.34740/kaggle/dsv/13566079
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.gyfhza
title: Occurrence Download

description: A dataset containing 3830 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Gentiana lutea"
 ]
}

 The dataset includes 3830 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009487-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0jq1147
title: CIL:39602, Saccharomyces cerevisiae. In Cell Image Library

description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please read the microscopy section of the referenced paper for details before image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cln1. Cln 1 is a cyclin-dependent protein kinase regulator. These phase and GFP z-series images are part of an image group containing CIL 39601-39605. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP
DOI: 10.6075/j0rf5tb2
title: CIL:41606, Cricetulus griseus, epithelial cell, ovary. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: squash preparation
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 Transmission EM of whole mitotic metaphase chromosomes from Chinese hamster ovary cells. This image was recorded at a specimen tilt of 58 degrees and is grouped with one taken at 48 degrees, creating a stereo pair giving an oblique 3D view of the chromosomes.
description: CHO cells arrested at metaphase with colcemid were treated with 67% D2O, in 0.07M phosphate buffer and squashed in 50% acetic acid. Preparations were transferred to EM grids and examined with the Wisconsin HVEM operated at 1MeV.
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.
DOI: 10.6075/j0ng4p73
title: CIL:45933, 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 25856 - 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/j08g8jh4
title: CIL:40507, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
description: Details of the binding of the carrier vesicle to a microtubule. Four bridges, thought to be cytoplasmic dynein arms, span the 40nm space between these two structures. The membrane of the vesicle has been fractured to expose its smooth E-face. TEM taken on 5/18/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 31,500X. 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/). Published in J. Cell Biol. 111:2553-2562, 1990. Adapted with permission.
DOI: 10.6075/j07w6bj5
title: CIL:38865, Didinium nasutum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: The division furrow of a dividing Didinium. A thick layer of epiplasm coated on the cytosolic side by mitochondria forms the constricting ring in the furrow. As usual mucocysts lie between the epiplasm and the pellicular membranes. The new cytopharynx in the opisthe already has lamellae and the alveolus seems to be absent from this region. The macronucleus is constricted in the furrow and elongated nucleoli are stretched out along microtubules are evident. TEM taken on 5/21/69 by R. Allen with Philips 300 operating at 60kv. Neg. 5,000X. The raw film was scanned with an Epson Perfection V750 Pro. This high resolution image is suitable for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j08g8jjk
title: CIL:11106, Rattus, ciliated epithelial cell. In Cell Image Library

description: Electron micrograph showing the brush border of intestinal epithelial cells of the rat. The parallel microvilli of the brush border are about 0.1 µm wide and 1.0 µm in length. Image by Jean Paul Revel and Sanford Palay, Figure 38 from Chapter 2 (Specializations of the Free Surface) 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.
description: Preparation: crosslinking-fixative fixed tissue; osmium tetroxide 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
DOI: 10.6075/j0p84b02
title: CIL:12958, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and GOLPH3 (a trans-Golgi associated protein that can also be associated with mitochondria; smaller gold particles) staining. Note that trans‐Golgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to GOLPH3 (rabbit polyclonal GMx33) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 28,500 X. See Ladinsky and Howell (2007) for more information on methods used.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.34740/kaggle/dsv/13566088
title: Full TMDB Movies Dataset 2024 (1M Movies)
DOI: 10.5281/zenodo.17491555
title: Data of Quartiles of Procurement Clients and Procurement Data for Simitli and Etropole
DOI: 10.5281/zenodo.17491556
title: Data of Quartiles of Procurement Clients and Procurement Data for Simitli and Etropole
DOI: 10.6075/j0qf8rpj
title: CIL:11433, Amoeba. In Cell Image Library

description: Figure 241 from Chapter 7 (Mitochondria) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. The cristae of these mitochondria from Singh amoeba have a tubular appearance. Image by Tom Pollard. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
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
Data qualification: Processed
DOI: 10.6075/j0pg1rfs
title: CIL: 54032. 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: CAMK 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/j0v987f2
title: CIL:45855, 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 25492 - 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/j0w95852
title: CIL:36476, Xenopus laevis, fertilized egg. In Cell Image Library

description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
DOI: 10.6075/j0fj2ffz
title: CIL:37200, Cavia porcellus, pancreas. 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)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
description: References:
Palade, G.E. 1952. J. Exp. Med. 95:285-298.
Palade, G.E. 1952. Anat. Rec. 114:427-451.
Sabatini, D.D, K. Bensch and R.J. Barrnett. 1963. J. Cell. Bio. 17:19-58. 
Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification X12,100.
description: Transmission electron micrograph of guinea pig pancreas mitochondria and lipid droplets. The use of osmium tetroxide as a fixative for electron microscopy was first described by Dr. Palade at the Rockefeller. Another major advance in fixation for electron microscopy was done at Yale by David Sabatini who described the use of glutaraldehyde which not only preserved ultrastructure, but enzymatic activities which opened up the possibility of EM localization of enzymatic function in cells. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.