cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0gq6xf9
title: CIL: 53869, Homo sapiens, HeLa. In Cell Image Library

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.
description: OTHER 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/j05d8r1q
title: CIL:10545, 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
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Yellow fluorescent proteins from Aequorea; mCherryFP
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing YFP-tagged TgIMC1 (innermembrane complex scaffold protein) and mCherry-tagged human alpha1tubulin. Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 60X water immersion, 1.2 NA. Filters: mCherry, ex 555-592 em 600-665, YFP, ex 490-510 em 525-595. Captured with CoolSnapHQ/ICX285. Image stack corresponds to deconvolved stack: CIL# 10546, maximum projection stack: CIL# 10547 and raw data stack with DIC: CIL# 10542.

Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.6075/j0jq115p
title: CIL:42162, Homo sapiens, epithelial cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: multi-cellular tumor fragment
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: contrast adjustment
description: Time-lapse movie of a human tumor fragment grown in Matrigel that was freed and reembedded in Matrigel. Images collected every 15 minutes and bar is 50 microns. CIL 42162 (this movie) - CIL 42165 are related movies that show human tumor growth fragments grown in different matrices, freed, and then reembedded. This movie is part of a group of movies that include CIL 42151-42168.
DOI: 10.6075/j07p8xcn
title: CIL:35450, Mus musculus, early embryonic cell. In Cell Image Library

description: First cleavage of a live mouse zygote. Clear circles are the nuclei which are in a sea of granule dense yolk. The band around the two cells is the zona pellucida.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: single-spot confocal microscopy
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: fast Fourier filtered; contrast adjustments
Data qualification: Processed;spatialmeasurements
description: Fertilized mouse egg was kept at 37 degrees Celsius in a MatTek coverslip bottom dish on an inverted microscope stage. Imaged using a Leica SP2 AOBS confocal with a 488 nm laser and 10X or 20X objective lens. The pinhole was set to Leica's calculated size for 1 Airy unit, each Z section was scanned in one pass, and the bit depth was 8. Additional information may be found in the Leica generated meta text file attached to the image. Microscopy was performed at the Analytical Imaging Facility of the Albert Einstein College of Medicine.
DOI: 10.6075/j0wm1cjt
title: CIL:12027, 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: polarization microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: intrinsic birefringence
Visualization methods: relative retardation (retardance) measurement
Processing history: 5-frame algorithm
description: Movie of meiosis I, starting at metaphase in primary spermatocytes of the crane-fly Nephrotoma suturalis that have been experimentally flattened. 
Time-lapse polarization 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 immersion condenser, with 2.0x zoom lens. Images captured every 15 sec over 35 min using a QImaging Retigo EXi CCD camera. Raw images were processed 
using 5-frame algorithm (Shribak and Oldenbourg, 2003). The time series used for the movie is included in this grouped set.
DOI: 10.6075/j0js9p2x
title: CIL:49851, Mus musculus, multipolar neuron, M5 melanopsin retinal ganglion cell. In Cell Image Library

description: A whole, intact retina was isolated from an excised mouse eye and dissected away from the retinal pigment epithelium; the retina was flat mounted with the ganglion-cell side up onto a glass chamber and superfused with Ames' medium during ex-vivo patch clamp electrophysiological experiments as previously described (see Estevez et al., 2012, J. Neuroscience). The recording pipette of the cell contained Lucifer yellow dye which was dialyzed into the cell over the course of a 30 minute recording. At the end of the recording, the tissue was fixed with 4% paraformaldehyde in 0.1M phosphate buffered saline (PBS) for 45 minutes at room temperature. The tissue was washed 3 x 15 minutes in PBS, incubated for 2 hours in blocking solution (2% Triton X-100 and 5% donkey serum in PBS at 4℃) at room temperature and incubated with rabbit anti-lucifer yellow (1:500; Life Technologies, Carlsbad, CA) for 2 nights at 4℃. Then the tissue was rinsed 6 x 10 minutes in PBS and counterstained with donkey anti-rabbit alexa 488 (1:200; Life Technologies, Carlsbad, CA 1: 200) for two hours at room temperature. The immunostained retina was washed 3 x 15 minutes in PBS, mounted on a glass slide and coverslipped using Prolong Gold mouting medium (Life Technologies, Carlsbad, CA). 

Images were acquired with a Zeiss LSM 510 Meta laser scanning microscope with a plan-apochromat 20x/0.8 objective. The dye was excited with a 488 nm laser at 5% emission was detected through a 505-550 band pass filter and imaged at 12-bits. The image stack consisted of a 450 μm x 450 μm window through 14 stacks at 0.5 μm (total of 7 μm in z-depth) through the ganglion cell layer and ON-sublayer of the inner plexiform layer of the retina.
description: These color images show the three-dimensional morphology of an M5 melanopsin retinal ganglion cell from an ex-vivo isolated flat-mount mouse retina preparation. This retinal neuron was visually identified and targeted for patch clamp electrophysiological recordings based on somatic EGFP fluorescence expression the Opn4cre/+;Z/EG+/- mouse line as previously described (Ecker et al., 2010, Neuron). Lucifer yellow dye (green) was dialyzed into the cell by passive diffusion from the recording pipette to reveal dendritic morphology of the M5 cell.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: Cell is imaged within an isolated intact retina (ex vivo)
Imaging mode: Confocal laser scanning fluorescence microscopy
Parameter imaged: Fluorescence Emission from Alexa Fluor 488 dye
Source of contrast: distribution of dye
Visualization methods: Intracellular dye counterstained with a primary antibody plus labeled secondary antibody.
Processing history: unprocessed raw data
DOI: 10.6075/j0mk6cq4
title: CIL: 54607. In Cell Image Library

description: The biophysical properties of sensory neurons are influenced by their morphometric and morphological features, whose precise measurements require high-quality volume electron microscopy (EM). However, systematic surveys of these nanoscale characteristics for identified neurons are scarce. Taking advantage of the CryoChem method, which permits high-quality ultrastructural preservation of cryofixed and genetically labeled samples for volume EM, we acquired serial block-face scanning electron microscopy (SBEM) images of antennal tissues in which select ORNs expressed the APEX2 EM marker. These SEBEM datasets allow a systematic morphometric and morphological analysis of identified olfactory receptor neurons in Drosophila melanogaster.
description: Drosophila antennae were prepared as described in Tsang et al. After cryofixation by high-pressure freezing and freeze-substitution in a cocktail containing uranyl acetate and glutaraldehyde, cryofixed antennae were rehydrated gradually at ice temperature. Rehydrated samples were then subjected to DAB labeling reaction and stained using a high-contrast en bloc staining protocol. Next, the samples were dehydrated for resin infiltration and embedded in Durcupan epoxy, followed by imaging with X-ray microscopy and then serial block-face scanning electron microscopy.

The antenna was imaged using a Zeiss Gemini scanning electron microscope equipped with a Gatan 3View2XP and OnPoint backscatter detector. Images were acquired at 2.5 kV accelerating voltage with a 30 μm condenser aperture and 2.5 μsec dwell time; Z step size was 50 nm; pixel size was 3.85 nm; raster size was 20k x 13.75k; Z dimension was 999 sections, and variable pressure under nitrogen. Volume was aligned using cross correlation, segmented, and visualized using IMOD.
description: Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
DOI: 10.6075/j0251j8c
title: CIL:39622, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0df6pvd
title: CIL:36725, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: To label membranes inside the cell we used very lightly fixed cells (0.25% glutaraldehyde) that were then rapidly frozen in liquid nitrogen and sectioned later at -100oC. These frozen sections were picked up on drops of methylcellulose and transferred to a Formvar-supported grid. The sections were immunogold labeled (15nm gold) to show the location of the specific antigen inside the cell as well as on the cell surface. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This image is suitable for qualitative analysis. A high resolution version of this image in the library (CIL:40557) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Detail of acidosome docking sites at DV-IA planar view through the site where acidosomes are docked and/or fusing with a DV-I. These sites are labeled for the mAb specific for antigen L1. TEM taken on 9/27/93 by R. Allen with Zeiss 10A operating at 80kV. Neg. 15,900X. Bar = 0.25µm. Published in J. Cell Sci. 108:1263-1274, 1995, and adapted with permission.
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; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.15468/dl.pbhrvw
title: Occurrence Download

description: A dataset containing 1765 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus tabuliformis"
 ]
}

 The dataset includes 1765 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009374-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0n29vhh
title: CIL:46060, 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 26666 - 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/j03f4pq2
title: CIL:39552, 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 see the microscopy section in the referenced manuscript for details for image analysis.
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; visualization of contiguous regions
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged NET1. 
 
 NET1 is a core subunit of the RENT complex that involves in nucleolar silencing and telophase exit; stimulates transcription by RNA polymerase I and regulates nucleolar structure.
 
These phase,gfp images are part of an image group that ranges from CIL:39551-39555. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.6075/j00864m6
title: CIL:40398, Vibrio cholerae. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Scanning electron microscope image of Vibrio cholerae bacteria, which infect the digestive system.This image is part of an image group that includes CIL:40395-40399.
description: Relevant reference: T.J. Kirn, M.J. Lafferty, C.M.P Sandoe and R.K. Taylor, 2000, "Delineation of pilin domains required for bacterial association into microcolonies and intestinal colonization", Molecular Microbiology, Vol. 35(4):896-910

Complete specimen preparation protocol available at http://remf.dartmouth.edu:8080/EM-Wiki

Image collected on a Zeiss DSM 962 SEM
DOI: 10.6075/j0t72gbb
title: CIL:35674, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc6. Cdc 6 is an essential ATP-binding protein required for DNA replication, component of the pre-replicative complex (pre-RC) which requires ORC to associate with chromatin and is in turn required for Mcm2-7p DNA association; homologous to S. pombe Cdc18p.These phase,gfp images are part of an image group that ranges from CIL:35660-35679. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors 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; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0nk3d60
title: CIL:15460, Didinium nasutum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Cortex and cytoplasm of Didinium. This cell cortex image includes the extrusive organelles mucocysts involved in cyst formation and one cyrtocyst of unknown function. Also, a few ciliated basal bodies of one of thge two ciliated girdles of locomotor cilia. Further details available at Wessenberg, H. and Antipa, G. 1968. Studies on Didinium nasutum. I. Structure and ultrastructure. Protistologica 4:427-447. TEM taken in 1966 by G. Antipa with JEM T6S operating at 50kV. Neg. 6,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 90nm thickness.
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
DOI: 10.6075/j0930s17
title: CIL:35965, Cecidomyiinae, Lepidosaphes, sperm. In Cell Image Library

description: Figures 347 (upper) and 348 (lower) from Chapter 14 (Sperm Flagellum) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Sperm tail organization in some insects deviates from the organization observed in mammals. Upper: A cross section of sperm tail of the cecidomyid fly, Diplolaboncus tumorificus shows only an outer dynein arm (arrows) emerging from doublets of microtubules. Lower: Transverse sections through spermatozoa of the oyster shell scale insect, Lipidosaphes, shows singlet microtubules aranged in concentric rings around a central core. Upper micrograph courtesy for Romao Dallai; lower from Phillips, Spermiogenesis, Academic Press, New York, 1974. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed