cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0xs5tk6
title: CIL:12635, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the largest accumulation of endosomal vesicles and early endosomes is next to the buccal cavity area under the membranelles of the peniculi and quadrulus. Cilia of the peniculi have a very close packing but have only three rows of parasomal sacs, two rows on the two margins of the light rows of cilia and a third row down the middle of the eight ciliary rows separating the dorsal from the ventral peniculi. Early endosomes have smooth membranes except for their clathrin coated evaginations waiting to be pinched off. In this micrograph most membranes are uncoated. Two tangentially fractured basal bodies showing the globular masses seen in thin sections in their shafts are embedded in strands of the meshwork of the filamentous reticulum. Only one cilium shows the P-fracture face of the ciliary membrane, all others appear not to have been fractured. Rings of IMPs or transmembrane particles are seen at ciliary bases. TEM taken on 6/4/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X.The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.15468/dl.cjs6uj
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Hong Kong)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bauhinia variegata"
 ]
}

 The dataset includes 307 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009427-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0w66jqw
title: CIL:36465, Xenopus laevis, fertilized egg. In Cell Image Library

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: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
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/j0r78f8p
title: CIL:35834, Saccharomyces cerevisiae. In Cell Image Library

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 images are part of an image group containing CIL 35820-35839. 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
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.
DOI: 10.6075/j0n58mjq
title: CIL:50677, Drosophila melanogaster. In Cell Image Library

description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
DOI: 10.6075/j01z443x
title: CIL: 53792, Homo sapiens, HeLa. In Cell Image Library

description: NDK 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
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.
DOI: 10.6075/j0794382
title: CIL:45937, Homo sapiens. In Cell Image Library

description: Plate 25862 - 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.
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.
DOI: 10.6075/j0gt5mk1
title: CIL:45868, 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 25575 - 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/j0c53k50
title: CIL:38872, Euplotes sp., 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
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: Cirri arise from the ventral side and the adoral zone of membranelles circle the anterior end of the cell and curve ventrally along one side of the oral cavity. The AZM is composed of triplet rows of cilia in the anterior end of the cell. Cirri are composed of 8 or 9 rows of tightly packed cilia. The cell uses these cirri to crawl over the substrate. TEM taken on 7/24/67 by R. Allen with Philips 200 operating at 60kV. Neg. 1,370X. 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 film was scanned with a Nikon Coolscan 9000ED. This image is suitable for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0rn36gq
title: CIL:50520, ultrastructural features in AD neurons. In Cell Image Library

description: Item type: recorded image
Imaging mode: TEM
description: We observed several interesting ultrastructural features in AD neurons. These include associations of paired helical filaments (PHF) with the membranes of the nuclear envelope and with ribosomes, differences between the distribution of the Golgi apparatus in neurons containing paired helical filament bundles as compared to neurons without these filaments, and abnormalities in the microtubules of neuronal processes in the vicinity of neuritic plaques.
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer‚Äôs disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope. Stereo viewing and computer assisted serial reconstruction techniques were employed to visualize three-dimensional relationships among cytoplasmic components of cortical neurons.
DOI: 10.6075/j0ft8jqt
title: CIL:27854. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.15 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.13140/rg.2.2.24061.78567
title: 3D Reconstruction. Design patent RU 139010
DOI: 10.6075/j0n0167b
title: CIL: 54164. 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: Visualization methods: confocal microscopy
description: TK 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.
DOI: 10.6075/j05b02kw
title: CIL:40217, Mus musculus, Neuroblastoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); Fluorescein (FITC)
Data qualification: Processed
description: Wide field fluorescent image of cultured neuroblastoma cells labeled with phalloidn FITC (green) and DAPI (blue) nuclear stain. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For further information, see Weimiao Yu, Hwee Kuan Lee, Srivats Hariharan, Wen Yu Bu and Sohail Ahmed. Evolving Generalized Voronoi Diagrams of Active Contours for Accurate Cellular Image Segmentation. Cytometry Part A 77A pg. 379~386, 2010.
description: NIE115 neuroblastoma cells were grown on 18 X 18 mm lamin coated glass coverslips maintained at 37 deg C in 5% CO2. Culture medium was Dulbecoo's Modified Eagle's medium supllemented with 4500 mg/ml glucose and 1% penicillin-streptomycin as an antibiotic. Cells were serum starved for 48 hrs and then fixed with 4% paraformaldehyde, then counterstained with DAPI and FITC-phalloidin. Images were acquired with a Zeiss epifluorescence microscope and a 20X objective.
DOI: 10.6075/j0j102q0
title: CIL: 52730, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=3, z=12 from PS11_10021_2B_Myc_Terc
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
DOI: 10.6075/j0jw8df6
title: CIL: 52548, 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: Tile x=7, y=1, z=19 from BL32077_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.23729/fd-4d351479-3883-3759-aa4d-3dd634e08e36
title: Baltic Sea Sediments: KU-A

description: First set of three sets of KU samples of the 'Baltic Sea Sediments' data set. Preview dataset found at https://doi.org/10.23729/fd-2a34834d-4308-3575-8045-c34c65ecca30 . To obtain data, please contact fairdata-pas@gtk.fi .
DOI: 10.5281/zenodo.17491115
title: Dataset for Political Adv.
DOI: 10.5281/zenodo.17491116
title: Dataset for Political Adv.
DOI: 10.6075/j0s181xg
title: CIL: 50723, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 6.5_Cell_6_Surface_Rendering. In Cell Image Library

description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Mictoscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
6.5_Cell_6_Surface_Rendering is a compressed (zipped) folder containing all files required to render the surface of the bundle. Also included is the ‘ProjectLog’ file produced by Slice and View acquisition software.
This file is a part of Dataset 6, comprised of files related to the Cell #6 of current study. The numbering order of the files reflects the order of operations performed during the analysis. The raw imaging data related to this cell was deposited within Dataset 1 (CIL:50680).