cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0fb51ww
title: CIL:25314, Drosophila melanogaster, fat body cell. In Cell Image Library

description: Fat body cells from larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated, transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film, are transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. 

Image shows a series of bands and interbands in a polytene chromosome. This image was taken with a tilt angle of 55 degrees. The accompanying grouped image, taken at 45 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0qj7g2t
title: CIL:25303, Drosophila melanogaster. In Cell Image Library

description: Movie of colchicine-induced depolymerization of the metaphase spindle in a Drosophila S2 cell expressing GFP-tubulin. 
Images were recorded at 120 sec intervals using a spinning disc confocal microscope on a Nikon TE-200 stand with a 100x 1.4 NA Plan APO DIC objective lens and recorded with a Hamamatsu Orca-ER CCD. See Supplemental Video 3 in Maresca and Salmon, 2009 J Cell Biol 184:373-281.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Green fluorescent proteins from Aequorea
Processing history: unprocessed raw data
DOI: 10.6075/j0v40t0h
title: CIL:25305, Drosophila melanogaster. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Green fluorescent proteins from Aequorea
Processing history: unprocessed raw data
description: Confocal fluorescent time-lapse imaging of bipolar spindle collapse induced by 1 uM taxol in a
mitotic Drosophila S2 cell expressing GFP-tubulin. Images were recorded at 120 sec intervals using a spinning disc confocal microscope on a Nikon TE-200 stand with a 100x 1.4 NA Plan APO DIC objective lens and recorded with a Hamamatsu Orca-ER CCD. See Supplemental Video 6 in Maresca and Salmon, 2009 J Cell Biol 184:373-281.
DOI: 10.6075/j0125rh5
title: CIL:25302, Drosophila melanogaster. In Cell Image Library

description: Movie of metaphase through the onset of cytokinesis in Drosophila S2 cells expressing GFP-tubulin. Images were recorded at 60 sec intervals using a spinning disc confocal microscope on a Nikon TE-200 stand with a 100x 1.4 NA Plan APO DIC objective lens and recorded with a Hamamatsu Orca-ER CCD. See Supplemental Video 2 in Maresca and Salmon, 2009 J Cell Biol 184:373-281.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Green fluorescent proteins from Aequorea
Processing history: unprocessed raw data
DOI: 10.6075/j0s181f6
title: CIL:24981, Drosophila melanogaster, fat body cell. In Cell Image Library

description: Fat bodies from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin and stained with uranyl acetate, embedded in epoxy resin, and 0.5 micrometer sections prepared
(see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. 

Image shows a series of bands and interbands in a polytene chromosome. This image was taken with a tilt angle of +5 degrees. The accompanying grouped image, taken at -5 degrees forms a stereo pair, providing a 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0wm1cb4
title: CIL:24967, Drosophila melanogaster, fat body cell. In Cell Image Library

description: Fat bodies from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin and stained with uranyl acetate, embedded in epoxy resin, and 0.5 micrometer sections prepared
(see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV. The image shows a band-interband-band region of polytene chromosome taken with a tilt angle of +5 degrees. The accompanying grouped image, taken at -5 degrees forms a stereo pair, providing a 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0rn36mh
title: CIL:24920, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: HeLa cells expressing Myc-GnT1IP-L (Myc-tagged GlcNAcT-1 inhibitory protein, long transcript, membrane-anchored) (red) were treated with cycloheximide and brefeldin A to cause retrograde transport of Golgi enzymes into the ER. Endogenous alpha-mannosidase II (ManII, green) was relocalized to the ER by BFA treatment and GnT1P-L was also found in the ER and some was observed at ER exit sites (shown in Fig 4D, J Cell Biol. 190: 893-910, 2010.). Transiently expressed Myc-GnT1IP-L is normally primarily localized in the Golgi and ERGIC and partially in the ER (shown in Fig 4; J Cell Biol. 190: 893-910, 2010.). Transfected HeLa cells were fixed in 3% paraformaldehyde, blocked with 0.2% Triton X-100, 1% FBS, 0.5% BSA in PBS with Ca[2+] and Mg[2+], followed by incubation in primary antibodies (anti-Myc mouse mAB, 9E10 (Covance) and anti–human ManII rabbit pAb) and secondary antibodies (Alexa 568 and Alexa 488) and DAPI (blue) to stain nuclei. Cells were mounted using Fluoromount (SouthernBiotech). Immunofluorescent images were digitally acquired on an inverted microscope (Axiovert 200M; Carl Zeiss, Inc.) coupled to a 12-bit cooled charge-coupled device camera (AxioCam MRm Rev. 3; Carl Zeiss, Inc.) controlled by Axiovision software (AxioVs40, version 4.7.2.0; Carl Zeiss, Inc.), using a 100x/1.3 NA oil immersion objective (EC Plan-NeoFluar; Carl Zeiss, Inc.), and saved as tiff files (1388 × 1040, 8 bit). All pictures were treated identically using Adobe Photoshop to remove background and adjust contrast. This image corresponds to Figure 5E, top panel (merge) in J Cell Biol. 190: 893-910, 2010. Images in Fig 5 include CIL#s 13658, 24919, 24920.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; c-MYC peptide tag
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j08k77xf
title: CIL:24819, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Intracellular localization of GFP-GOLPH3 in BY4742 vps74∆ sac1∆. SAC1 encodes an integral membrane phosphoinositide phosphatase and in the sac1∆ vps74∆ mutant, GFP-GOLPH3 localizes, in addition to the Golgi apparatus, to nuclear ER and cortical ER and/or PM. Control image for images showing ectopic expression of GFP-GOLPH3 with mutations in the sulfate-binding pocket (CIL#s 24820, 24821). This study demonstrates that the sulfate-binding pocket of Vps74 and GOLPH3 mediates PtdIns4P-binding and is essential for function. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4A GFP-GOLPH3 wild-type/sac1∆ panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4A include CIL#s 13449, 13451, 13453, 13455, 13456, 13457, 24816, 24817, 24818, 24819, 24820, 24821.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0fn14sc
title: CIL:46048, Homo sapiens. In Cell Image Library

description: Plate 26622 - 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/j0br8rxc
title: CIL: 54497, Homo sapiens. In Cell Image Library

description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for hematoxylin and eosin.
description: Imaging mode: bright-field microscopy
Visualization methods: hematoxylin and eosin
DOI: 10.6075/j07p8x32
title: CIL:38709, Chlamydomonas reinhardtii. In Cell Image Library

description: Isolated chloroplas tmembranes of the unicellular photosynthetic alga Chlamydomonas reinhardtii were fixed, sectioned, and examined by transmission electron microscopy. In this ac-5 mutant, regions of stacked and unstacked thylakoids are seen. The section also includes osmiophilic globules (G), a mitochondrion (M) and dictyosome (D) See Fig 11 in Goodenough and Staehelin 1971 J Cell Biol 48:595-619.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-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; uranyl salt; lead salt
Data qualification: Processed
description: Isolated chloroplast membranes were fixed with glutaraldehyde, post fixed with osmium tetroxide, dehydrated, embedded in epoxy resin, and thin sections cut, stained and examined with a Hitachi HU-11C TEM.
DOI: 10.6075/j0pg1r73
title: CIL: 51986, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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: 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: 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: 10.15468/dl.f8cbrg
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Arthraxon hispidus"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009299-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0bc3z3d
title: CIL: 52540, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=7, y=1, z=11 from BL32077_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
DOI: 10.6075/j0hh6hxv
title: CIL:39061, Bos taurus, blood vessel endothelial cell. In Cell Image Library

description: B0007569 Confocal micrograph 2009. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 488; CMX rosamine (Mitotracker Red)
Processing history: unprocessed raw data
description: This image shows a bovine pulmonary artery endothelial cell. The pulmonary artery is the large vessel that takes deoxygenated blood cells from the heart to the lungs. These cells have been stained with DAPI to highlight the nucleus (blue), MitoTracker Red CMXRos to stain mitochondria (red dots), and Alexafluor 488 phalloidin to label F-actin filaments in the cell that make up the cytoskeleton.
DOI: 10.6075/j0j67g2t
title: CIL:10525, Toxoplasma gondii RH. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: fluorescence microscopy; time lapse microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; mRFP1
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
description: Time-lapse of Toxoplasma gondii infection of human foreskin fibroblast cells. T. gondii stably express EGFP-tagged TgIMC1 and mRFP-tagged TgMORN1 (MORN domain containing protein). Formation of daughter cells is visible during time-lapse. Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 60X water immersion, 1.2 NA. Filters: EGFP, ex 450-490 em 500-540, mRFP, ex 555-592 em 600-665. Dichromatic mirror: Chroma 89021. Captured with CoolSnapHQ/ICX285. 3D stacks of images were collected at 0.6 μ increments in z, every 10 min. Maximum intensity projection of 3D deconvolved stacks at each timepoint were used to generate mpg movie. Corresponds to raw data: CIL# 10525. and 3D deconvolved data: CIL# 10523 and projection of 3D deconvolved data: CIL# 10524. 

Unpublished image that is similar to images published in PMID: 16518471 and 20140195. See publications for other experimental details.
DOI: 10.6075/j0c82903
title: CIL: 53804, 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: 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
DOI: 10.6075/j02f7n6r
title: CIL: 54364. 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: Atypical 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.