cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0b85866
title: CIL:39541, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP taggedMAD2. 
 
MAD2 is a non-essential gene that encodes a component of the spindle checkpoint. The spindle checkpoint delays the onset of anaphase in cells with defects in mitotic spindle assembly or in the attachment of chromosomes to the spindle microtubules. The checkpoint works by inhibiting the activity of the anaphase promoting complex, thereby preventing the degradation of several cell cycle regulators. Like other spindle checkpoint mutants, mad2 loss-of-function mutants are sensitive to benomyl and cannot delay cell division in response to spindle depolymerization. Mad2p forms a tight complex with another spindle checkpoint protein, Mad1p, throughout the cell cycle. Mad2p also forms a complex with Cdc20p, which activates the anaphase promoting complex, and Mad3p; the presence of Mad1p is required for the complex to form. Bub1p, Bub3p, Mad1p, Mad2p, Mad3p, and the protein kinase Mps1p act in a branch of the spindle checkpoint pathway that may prevent premature chromosome disjunction. A second branch involves Bub2p and Bfa1p, and may prevent cytokinesis prior to chromosome segregation. Homologs of Mad2p act in the spindle checkpoint in Xenopus (Xmad2) and human (MAD2L1 andMAD2L2.MAD2 was originally identified as the open reading frame YJL031C. However, it is now known thatMAD2 corresponds to the adjacent open reading frame YJL030W, while YJL031C encodes the geranylgeranyltransferase subunit Bet4p.
 
These phase,gfp z-series images are part of an image group that ranges from CIL:39541-39545. 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
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.
DOI: 10.6075/j0qc02ch
title: CIL:39021, lung cancer cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions
Processing history: colorized
description: B0007782 Lung cancer cells. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Colorized scanning electron micrograph showing two lung cancer cells. These cells were grown using cell culture techniques.
DOI: 10.6075/j0bc3xpm
title: CIL:21791, Drosophila melanogaster, epithelial. In Cell Image Library

description: Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA, CIL 21789) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2, CIL 21749, 21739, 21759, and 21773, respectively) has a different gene knocked down by RNAi. This is the set of wild-type cells. There are 10 images of each sample, for a total of 50 images. The images were acquired on a Zeiss Axiovert 200M microscope. A recommended use for these five image sets is to algorithmically compute the number of cells in each image. A tab-delimited text file containing this information can be found at the URL indicated in the attribution box. The recommended citation when using these images is: "We used the Drosophila Kc167 1 image set (Carpenter, et al., Genome Biology, 2006) available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: 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 DNA
Visualization methods: Hoechst 33342
Processing history: unprocessed raw data
DOI: 10.6075/j01g0k2h
title: CIL:35958, Cricetulus griseus, sperm. In Cell Image Library

description: Figure 329 from Chapter 14 (Sperm Flagellum) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. This electron micrograph shows a transverse section through the midpiece of Chinese hamster spermatozoa. Image by David Phillips. 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
DOI: 10.6075/j0w37vgt
title: CIL:10420, Gallus gallus, erythrocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM); darkfield illumination
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Nucleated erythrocytes from chicken were spread on water, the dispersed chromatin picked up on carbon-formvar grids, fixed with paraformaldehye, critical point dried and shadowed with platinum. Images were obtained with the Wisconsin high voltage TEM at 1MEV using darkfield illumination. For this micrograph, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees providing a stereo pair with an oblique 3D view of the tangled and irregular chromatin fibers is grouped with this image.
DOI: 10.6075/j0x066dz
title: CIL:45765, Homo sapiens. In Cell Image Library

description: Plate 20633 - 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/j0z89bpd
title: CIL:1734, 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 2 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: 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
DOI: 10.6075/j0g73cv3
title: CIL:9701, Coleps hirtus, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Oblique section of the Coleps contractile vacuole pore revealing the supporting microtubules and adjacent fibrous layer. 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 3/4/69 by R. Allen with Philips 300. Neg. 25,100X. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:9255) 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: film; print from negative was scanned for photoshop
DOI: 10.6075/j0ns0t06
title: CIL:10726, 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); Processed image based on 4 recorded images
Imaging mode: polarization microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: intrinsic birefringence
Visualization methods: relative retardation (retardance) measurement
Processing history: 4-frame algorithm
description: Time series of anaphase A and B of meiosis I in primary spermatocytes of the crane-fly Nephrotoma suturalis. 
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 imm. condenser, with 2.0x zoom lens. Images captured every 30 sec over 60 min using a QImaging Retigo EXi CCD camera. Raw images were processed 
using 4-frame algorithm (Shribak and Oldenbourg, 2003). A movie of this time series is included in this grouped set.
DOI: 10.6075/j05h7gd0
title: CIL:42166, Mus musculus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: mammary tumor organoid
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: Representative time-lapse movie of a mouse mammary tumor fragment in Matrigel. CIL 42167 is a related movie of a mammary tumor fragment in collagen I. Images collected every 20 min. This movie is part of a group of movies that include CIL 42151-42168.
DOI: 10.6075/j0jq108m
title: CIL:1755, 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: 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 2 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
DOI: 10.15468/dl.t58qrg
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Bupleurum densiflorum"
 ]
}

 The dataset includes 21 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009243-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0pr7v3k
title: CIL:12326, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: This group represents a serial series of sections. At the level of this section, the macronucleus and micronucleus are present. In the buccal cavity a row of paroral cilia is seen to separate the buccal cavity from the beginning of the cytopharynx. The spongiome of CV, membranelles of perioral ciliature, oral cilia, and the microtubules bordering the ventral wall of the BC are all evident. TEM taken on 3/12/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,800X. Bar = 2µm. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared thicker to accommodate the series. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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 scanned for Photoshop
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j03b5zbs
title: CIL:12325, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The contractile vacuole may evacuate through a CV pore located in an indentation of the pellicle not far from the adoral end. TEM taken on 3/18/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 5,000X. Bar = 1µm. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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 scanned for Photoshop
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0bc3xq2
title: CIL:12323, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: This group represents a serial series of sections. At the level of this section the funnel shaped oral region is now reduced to a narrow cytopharyngeal tube extending toward the aboral region of the cell. A few cross-sectioned cilia are present in the tube. Remnants of food vacuoles fill the cell's aboral half. Six membranelles of the perioral ciliature are present as well as the macronucleus. TEM taken on 3/12/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,800X. Bar = 2µm. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared thicker to accommodate the series. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j08k786f
title: CIL:12313, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm.
description: Detail of CV pore. Microtubules encircle the pore wall and other microtubules radiate out from the pore toward the CV membrane. TEM taken on 3/27/69 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. There is a high resolution version of this image in the library (CIL:39339) which 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; 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;spatialmeasurements
DOI: 10.6075/j0fq9vss
title: CIL:12311, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: Detail of cytopharyngeal vesicles. TEM taken on 3/2/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. 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:7665) 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 75nm.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).