cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0jq0zzs
title: CIL:27225, Fundulus heteroclitus, epidermal cell. In Cell Image Library

description: Cell junctions formed between adjacent epidermal cells in Fundulus heteroclitus scales. Desmosomes line the membranes of two epidermal cells. A vast network of intermediate filaments and microfilaments are present throughout the cytoplasm and connect to the desmosomes plates. Microtubules are also visible in the cells.
description: Fundulus heteroclitus scales were chemically fixed with 2.5% glutaraldehyde, 2% formaldehyde in 0.1M cacodylate buffer (pH 7.3), then post-fixed in 4% osmium tetroxide and stained en bloc in 1% uranyl acetate. The scales were then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph was imaged using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80 kV.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; dehydrated in ethanol
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: uranyl salt; lead salt
Processing history: unprocessed raw data
DOI: 10.6075/j0gm86rc
title: CIL: 51826, 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: 10.6075/j02f7mrh
title: CIL:39503, Vorticella microstoma, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Freeze fracture of Vorticella microstoma. This cell had been placed in a relaxing medium of saturated sodium pyrophosphate plus 0.01M EDTA (Stain Tech. 47:37, 1972) for 3 hours. A myoneme enclosed by ER membrane is fractured at the cell‚Äôs periphery. In this cell it appears that the ER wraps around the myoneme. The P-fracture face of the plasma membrane is studded with many IMPs of significant size in contrast to the E-face of the outer alveolar membrane which has few IMPs. Bits of the P-face of the inner alveolar membrane 
 show many IMPs on that face also. The P-face of the cytosolic-touching membrane of the ER and the E-face of the myonemal-touching membrane of the ER are visible. Linear arrays of IMPs on the E-face next to the myoneme may be transmembrane proteins associated with the linkage complex. Mitochondria are the most prominent organelles in the cytosol and their tubular cristae sometimes show signs of decoration with F1F0 ATP synthases. large arrow, direction of shadowing of freeze fracture replica. TEM taken on 11/11/75 by R. Allen with JEM 100B operating at 80kV. Neg. 11,015X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0q81cfg
title: CIL:45900, Homo sapiens. In Cell Image Library

description: Plate 25678 - 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/j0bp0208
title: CIL:16245, Mus musculus, CNS neuron (sensu Vertebrata), interneuron, hippocampal granule cell. In Cell Image Library

description: Distribution of interneurons expressing EGFP from the GAD65 promoter in the day 14 mouse hippocampus colabelled for the CB1 cannabinoid receptor (red) and counterstained with DAPI (blue) to show the cell layers. EGFP expression was amplified with chicken anti-GFP (Abcam, 1:2000). GAD65-EGFP expressing neurons are enriched in the dentate gyrus and a band of EGFP is present in the inner dentate molecular layer. CB1 immunoreactivity (L15 rabbit polyclonal 1:200, K. Mackie) is prominent in the molecular layer but also present at lower levers in the outer portion of the dentate molecular layer. Diffuse CB1 immunoreactivity is also present in the hilus. Section (40 um) was mounted with Fluoromount G and imaged with a 10X, 0.3 NA objective on a Zeiss Axiovert microscope. AF568 was excited at 562/40 nm and emission collected at 624/40 nm with Semrock filters and a single band dichroic (530-585 nm reflected, 601-800 nm transmitted). AF488 was excited at 482/35 nm and emission collected at 536/40 nm with Semrock filters and a single band dichroic (446-499 nm reflected, 513-735 nm transmitted). DAPI was excited at 350/50 nm and emission collected at 460/50 nm with a CLP400 dichroic (Chroma). Single images were captured for each channel using a Zeiss Axiocam MR CCD and pseudo-colored using Axiovision. Linear background subtraction was used on the presented image.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: fluorescence microscopy
Imaging mode: recorded image
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 488; Alexa Fluor 568
Processing history: unprocessed raw data
DOI: 10.6075/j0pv6j96
title: CIL:35667, Saccharomyces cerevisiae. In Cell Image Library

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
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.
DOI: 10.6075/j0959g79
title: CIL:28721. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.60 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6084/m9.figshare.30497175
title: Additional file 4 of Genetic architecture of resistance to plant secondary metabolites in Photorhabdus entomopathogenic bacteria

description: Supplementary material 4.
DOI: 10.6084/m9.figshare.30497175.v1
title: Additional file 4 of Genetic architecture of resistance to plant secondary metabolites in Photorhabdus entomopathogenic bacteria

description: Supplementary material 4.
DOI: 10.6084/m9.figshare.30497178
title: Additional file 5 of Genetic architecture of resistance to plant secondary metabolites in Photorhabdus entomopathogenic bacteria

description: Supplementary material 5.
DOI: 10.6084/m9.figshare.30497178.v1
title: Additional file 5 of Genetic architecture of resistance to plant secondary metabolites in Photorhabdus entomopathogenic bacteria

description: Supplementary material 5.
DOI: 10.6075/j0rr1zb9
title: CIL:39637, Saccharomyces cerevisiae. In Cell Image Library

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: 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: 10-hour timelapse of the double mutant Clb2dbŒî, Clb5Œî, which has the destruction box region of the CLB2 gene, on the cell cycle control system in budding yeast. The yeast, Saccharomyces cerevisia, are growing in 2% raffinose, since this mutation is inviable in glucose. The images from two experiments done with Wild-type Saccharomyces cerevisiae as a control 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/j04m93gt
title: CIL:36112, damselfly, flight muscle cell. In Cell Image Library

description: Longitudinal and cross sections showing ribbon like myofibrils regularly alternating with layers of mitochondria and SR/T tubules. Dyads are located in a grove of the mitochondrial surface. Negatives aere scanned on nikon 8000 at 4000dpi/6.3 micron scan step size, then reduced in size 4X for upload, for an effective pixel size of 25 micron.
 
 Technical details:
 Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer (pH7.2). Stored at 4C for several days. Muscle dissected out. Rinsed 3Xin buffer, postfixed in 2% PsO4 in buffer, for 1.5 hrs; rinsed 3 times in water, en-block stained in saturated aqueous uranyl acetate, embedded in Spurr. Thin sections stained in uranyl acetate and lead and examined in a Philips 410 Microscope.
 
 Reference for the image:
Loesser, K.E., Castellani, L. and Franzini-Armstrong, C. Disposition of junctional feet in muscles of invertebrates. J. Muscle Research Cell Motility 13:161-173, 199
description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0c53kxv
title: CIL:39955, Mus musculus, Purkinje cell. In Cell Image Library

description: Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
description: Tissue was perfused with paraformaldehyde, sectioned (100 µm) on a vibratome and mounted in gelvatol, and imaged on a Biorad Radiance 2000 Confocal using a 60x 1.4NA objective.
description: A Purkinje neuron from the cerebellum of a 2 month old male C57BL/6 mouse, injected with Lucifer Yellow. The elaborate, highly branched dendritic arbor is revealed in this maximum projection image which was generated by compiling a z-series of optical sections. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
DOI: 10.6075/j01c1w6c
title: CIL:41308, Penta lanceolata. In Cell Image Library

description: Scanning electron microscope image of Penta lanceolata anther (pollen bearing part of the stamen).
description: Image collected on a Zeiss DSM 962 SEM. See detailed protocol at http://www.dartmouth.edu/~emlab/manuals/sempreps/index.html
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; ethanol dehydration
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 deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0zc81h3
title: CIL:37215, Rattus, neuron. In Cell Image Library

description: Preparation: chemically fixed tissue
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
Processing history: unprocessed raw data
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification x13,200.
description: Transmission electron micrograph of nerve terminals from a rat tongue. 
 Note that this very early (1953) micrograph is primarily of historical interest since it pre-dates glutaraldehye fixation which was introduced in the early 60's and is considered essential for adequate nerve tissue preservation. Examples of nerve tissue micrographs prepared in 1965 are CIL:37218, CIL:37219 and CIL:37220. 
 Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0zp44wv
title: CIL:12412, Cricetulus griseus, epithelial cell. In Cell Image Library

description: Localization of MIIA/B (head, actin-binding domain of MIIA (myosin IIA), and tail domain of MIIB (myosin IIB)) in MIIA-deficient CHO.K1 cells. This Video corresponds to Fig. 10 A and video 5 from JCB 183:543-554 , 2008. Images of GFP-MIIA/B (green) and paxillin-mOrange (magenta) were collected every 4 s using TIRF microscopy with 10 frames/s shown. Images were acquired in an inverted microscope (model IX70;Olympus). For dual GFP- mRFP/mCherry/mOrange, a dual-emission filter (z488/543) was used. Images were acquired with a charge-coupled device camera (Retiga Exi; Qimaging) and analyzed using MetaMorph software (MDS Analytical Technologies).
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: TIRF
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; mOr
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.15468/dl.2b67gt
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Populus nigra thevestina"
 ]
}

 The dataset includes 24 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009309-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29368260
title: Additional file 4 of Integrating differential expression under drought with gene family expansion unique to drought-tolerant species prioritizes candidate genes for drought adaptation in Brassicaceae species

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.29368254
title: Additional file 2 of Integrating differential expression under drought with gene family expansion unique to drought-tolerant species prioritizes candidate genes for drought adaptation in Brassicaceae species

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.29368254.v1
title: Additional file 2 of Integrating differential expression under drought with gene family expansion unique to drought-tolerant species prioritizes candidate genes for drought adaptation in Brassicaceae species

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.29368257
title: Additional file 3 of Integrating differential expression under drought with gene family expansion unique to drought-tolerant species prioritizes candidate genes for drought adaptation in Brassicaceae species

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.30497235
title: Additional file 2 of Genetics of reproductive performance across Porcine Reproductive and Respiratory Syndrome (PRRS) outbreak phases in purebred and crossbred sows

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.30497235.v1
title: Additional file 2 of Genetics of reproductive performance across Porcine Reproductive and Respiratory Syndrome (PRRS) outbreak phases in purebred and crossbred sows

description: Supplementary Material 2
DOI: 10.5281/zenodo.17489848
title: Ped-sim def files and simulated segments from 100,000 pairs of 1st through 8th cousins

description: Ped-sim simulates IBD segments (and/or genetic data) for relatives. This repository includes Ped-sim def files for simulating 1st through 8th cousins (3rd through 17th degree relatives), including both full and half-relatives. It also contains simulated IBD segments from 100,000 pairs for each relationship using these def files and summary statistics of the IBD sharing between pairs in the .tot files. Pairs with zero IBD shared are not present in these files. See README.md in ped-sim-defs.zip for bash code used to simulate and to generate the .tot files.

The data were generated using four different crossover models: sex-specific genetic maps + crossover interference (ss_intf), sex-averaged map + crossover interference (sa_intf), sex-specific genetic maps + Poisson crossover localization (ss_poiss), sex-averaged map + Poisson crossover localization (sa_poiss).