cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03r0rkp
title: CIL:13900, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Saccharomyces cerevisiae (WT BY4741-MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0), transformed with EGFP-Atg8p, undergoing chronological aging on small synthetic 2% glucose media (SMD) without supplementation of spermidine. Image represents yeast morphology, visualized by DIC. DIC image was captured using a widefield microscope (Axioskop; Carl Zeiss, Inc) fitted with a Plan Neofluar 63× 1.25 NA oil immersion objective. Image acquired with a camera (SPOT 9.0 Monochrome 6; Diagnostic Instruments, Inc) using Metamorph software (Universal Imaging Corp) and processed with IrfanView and Photoshop (CS2; Adobe) software. Specifically, picture processing involved coloring and cropping of representative areas and was performed with IrfanView. In addition, linear adjustments of contrast and brightness were applied with Photoshop (using equal adjustment parameters for all pictures); no explicit γ correction was used. Image: Figure 2A, WT/Co/DIC panel, in Morselli et al. J Cell Biol 192: 615-629
description: Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Processing history: brightness and contrast adjusted
Data qualification: Processed
DOI: 10.6075/j0w66khm
title: CIL: 54519. 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: 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.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0668bw6
title: CIL:13874, Saccharomyces cerevisiae. In Cell Image Library

description: Tem1 (green) constitutively targeted to spindle pole bodies in nud1-2 cells at the restrictive temperature still displayed problems positioning the spindle (this image shows a rebudded cell, CIL #13873 shows an aligned spindle and CIL# 13889 shows a misaligned spindle) typical of nud1-2, despite the fact that viability was restored. Nud1 is required for mitotic exit and constitutive targeting of Tem1 recovered the mitotic exit defect of nud1-2 cells. DAPI (blue) and differential interference contrast (DIC) image are also shown. Image is Fig 7F, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 7 include CIL #13888, 13872, 13813, 13889, 13874.
description: Cells (MATa nud1::kanMX4 leu2::nud1-2::LEU2 pRS316::eGFP-CNM67–TEM1) grown at restrictive temperature 37C were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; boundaries between regions with different refractive index; compartmentalization of stain or label
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.15468/dl.p722d4
title: Occurrence Download

description: A dataset containing 8771 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Europe",
 "Geometry POLYGON((-8.74338 62.39326,-25.7167 38.16638,58.85977 24.67476,75.68802 79.65673,25.61961 73.10194,24.86785 70.40071,29.02113 63.44147,28.3286 60.40498,20.49221 58.86943,18.73479 56.2729,13.14905 54.83769,5.14987 54.41174,-8.74338 62.39326))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chenopodium album"
 ]
}

 The dataset includes 8771 records from 179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009369-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0jq0zm9
title: CIL:45930, 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 25853 - 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/j04m93ph
title: CIL:9712, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A view near the oral apparatus of Coleps and the attachment site of a microtubule filament bundle, fibrous interconnections, and a rod near a basal body that is out of the section plane in this TEM. Discoidal vesicles probably involved in digestion are aligned along the inside edge of the rod as are the extrusive organelles, the toxicysts. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 5/28/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:9018) is available for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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; Print of negative scanned to Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j04b30wx
title: CIL: 52825, 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: 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=4, y=1, z=2 from PS11_167511L_Myc_Terc
DOI: 10.6075/j0j38rz4
title: CIL: 50846, Saccharomyces cerevisiae (baker's yeast, budding yeast), Mixed population of S. cerevisiae cells. In Cell Image Library

description: Wild type Saccharomyces cerevisiae cells (S228C background) were treated with 0.5 mM of sodium arsenite for 60 minutes. Then, samples were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
description: Treated cells were cultured in YPD medium and high pressure frozen in a Wohlwend Compact 3 machine,
 followed by a short freeze substitution protocol in 2% Uranyl acetate and embedded in HM20 resin. Sections of 70 nm thickness were then contrast stained with 2% Uranyl acetate and Reynold's lead 
citrate. Pictures were aquired in a Tecnai T12 TEM with a Ceta CMOS 16M camera.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0g73d26
title: CIL:41609, Cricetulus griseus, epithelial cell, ovary. In Cell Image Library

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.
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 49 degrees and is grouped with one taken at 59 degrees, creating a stereo pair giving an oblique 3D view of the chromosomes.
DOI: 10.6075/j0jh3jxf
title: CIL:13450, Saccharomyces cerevisiae S288c. In Cell Image Library

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
description: Kre2-GFP is efficiently maintained in the Golgi apparatus in BY4742 vps74∆ expressing wild-type, untagged, Vps74. Control image for images showing that localization of Kre2-GFP is lost when mutant forms of Vps74 (mutations in the sulfate-binding pocket) are expressed (CIL#s 13452, 13454). 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 Fig4C top panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4C include CIL#s 13450, 13452, 13454.
DOI: 10.6075/j0cr5smx
title: CIL:833, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Purified rabbit skeletal muscle myosin in 0.6M KCl was deposited onto mica flakes, quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope at 100 kev.

Images were recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED.

Note the classic appearance of the individual molecules with two globular heads (myosin subfragment 1) and the long rod-like tail.

LEFT image of a stereo pair.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons; widefield illumination; wide-field detection
Parameter imaged: electron density
Source of contrast: electron density; elevation
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0s46r0b
title: CIL:2605, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 12 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0pc31m2
title: CIL:1106, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 4 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
DOI: 10.6075/j0jm28s0
title: CIL:24493, Rattus norvegicus, epithelial cell. In Cell Image Library

description: Cells were grown on 100-mesh gold EM grids, and maintained at 15°C for 4 hours before plunge freezing in liquid nitrogen (BalTec HPM-010), followed by freeze-substitution (1% glutaraldehyde, 0.1% tannic acid in acetone, replaced with 4% osmium tetroxide and 0.01% uranyl acetate), then embedded in Epon-Araldite and sectioned at 250nm (UltraCut-UCT, Leica). Sections were transferred to formvar-coated copper-rhodium slot grids (EMS) and stained with 2% aqueous uranyl acetate and Reynold's lead citrate. Digital images were acquired at a magnification of 15,000X with an FEI Tecnai TF20 transmission EM. For additional details refer to: J. Cell Biol. 144 (6) 1135-1149.
description: Preparation: tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Raw
description: This image is from a tomogram through part of a Golgi ribbon from a normal rat kidney cell, generated using high voltage electron microscopy following incubation at 15°C to block transport out of the Golgi complex. Following temperature block, large bulging domains appear on the three trans-most cisternae. The sample was tilted at angles of 1.5° to obtain the series of images in this set, and used to obtain 3-dimensional reconstructions of the Golgi apparatus and contributed to findings reported in Ladinsky et al. (1999) Golgi structure in three dimensions: Functional insights from the normal rat kidney cell. J. Cell Biol. 144 (6) 1135-1149.
DOI: 10.6075/j0rx9b95
title: CIL:1658, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 0 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j0sq8z3s
title: CIL:11944, Chaetopterus pergamentaceus, oocyte. In Cell Image Library

description: See S. Inoue et al. 2001. Centrifuge polarizing microscope II. Sample biological applications. J Microsc 201:357-367.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: polarization microscopy
Parameter imaged: retardance
Source of contrast: intrinsic birefringence
Visualization methods: visualization of contiguous regions
Data qualification: Processed
description: The movie shows several sequences showing changes in birefringence in oocytes of the marine annelid Chaetopteris that had formed meiotic spindles before exposure to centrifugal force in the Centrifuge Polarizing Microscope developed by S. Inoue. Spindles appear dark or bright according to their directionality with respect to that of the polarized light.
DOI: 10.6075/j0862f4x
title: CIL:37210, Rattus, cardiac muscle cell. In Cell Image Library

description: Preparation: chemically 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
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Transmission electron micrograph of longitudinal section of rat cardiac muscle from the atrium. A of group of horizontally-running myofibrils is seen at the top. Also prominent are numerous glycogen granules (small darkly staining spheres), two atrial granules (larger homogeneously staing spheres) and a mitochondrion. 
 Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x46,000.