cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0959hsw
title: CIL:55662, Homo sapiens. In Cell Image Library

description: Scan 17_D_EP_B -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
DOI: 10.6075/j09885nm
title: CIL:39079, Triticum sp., leaf. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
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; osmium tetroxide
Data qualification: Processed
description: CD3 mutant wheat (deficient in chlorophyll b was germinated and grown for 6 days in the dark, greened at high light intensity for 4 days in the presence of chloramphenicol, then prepared for thin section electron microscopy. The chloroplast shows a rather disorganized internal structure although grana stacks of thylakoids (GT) and unstacked stromal regions (ST) are evident. Also seen are osmiophilic globules (PG). V, vacuole, PM, plasma membrane, CW, cell wall. This set of grouped images, which also shows freeze-fracture views, includes wildtype chloroplasts.
description: Leaf segments 1 cm from the tip were fixed with 2% glutaraldehyde, postfixed with 1% osmium tetroxide, dehydrated, and embedded in Spurrs resin. Thin sections were stained with uranly acetate and lead citrate and examined in a JEOL 100C transmission EM at 60 KV, and images recorded on film. See Fig 12 in K D Allen et al. 1988 Biogenesis of thylakoid membranes is controlled by light intensity in the conditional chlorophyll b-deficient CD3 mutant of wheat. J Cell Biol 107:907-919.
DOI: 10.6075/j0cc10cz
title: CIL: 53988, Homo sapiens, HeLa. 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: STE 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/j08k7833
title: CIL:2756, 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 8 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/j0rb73q1
title: CIL:18488, damselfly, flight muscle cell. In Cell Image Library

description: Most images show fractures through the outer membrane of mitochondria and SR/T tubules of dyads nestled in long grooves of the mitochondrial surface. All leaflets of the membranes appear in the images. This image is part of the group image CFA00512. TEM magnification 24400X. The negative film was scanned at LBL then reduced in size for upload. Scan step size is 6.3 micron, 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. pH 7.2. stored at 4C for several days. Muscle dissected out. Infiltrated in 30% glycerol in water. Frozen in liquid nitrogen cooled Freon, fractured in Balzers 400 Freeze-fracture, shadowed with platinum at 45o angle. Replicas were cleaned with Clorox (to remove tissue and with either sulfuric acid or NaOH to try removing the tracheolae. Replicas examined in a Philips 410 Microscope. Reference for these images: 
Takekura, H. and Franzini-Armstrong C. The structure of Ca2+ release units in arthropod body muscle indicates an indirect mechanism for excitation-contraction coupling. Biophys. J. 83, 83, 2742-2753, 2002.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: unembedded tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0gm879z
title: CIL:35627, 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; differences in amount of elastic light scattering
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 Cln2. Cln2 is a G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p).These phase,gfp images are part of an image group that ranges from CIL:35620-35639. 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/j0js9p3c
title: CIL:28754. In Cell Image Library

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 0.30 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)."
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
DOI: 10.6075/j0028rns
title: CIL:42158, Mus musculus, epithelial cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: mammary organoid
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: tdTomatoFP; EGFP
Processing history: contrast adjusted; confocal stack
description: Time-lapse movie showing extensive dissemination of myoepithelial cells from P-cadherin null epithelium, with gradual loss of myoepithelial coverage. The cells are expressing td tomato as a membrane marker and eEGFP-actin using a keratin-14 promoter. Images were collected every 20 minutes. The image size is 350 x 350 microns. This movie is part of a group of movies that include CIL 42151-42168.
DOI: 10.6075/j0qr4vqt
title: CIL:45975, 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 25988 - 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/j0222sm3
title: CIL:38994, nerve fiber. 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
Processing history: unprocessed raw data
description: Transmission electron micrograph showing a transverse section through a nerve fiber in the corneal stroma. The cell contains a nucleus, mitochondria and some rough endoplasmic reticulum. The nerve is passing through the layers of stromal lamellae, and layers of collagen fibrils lying across each other at different angles appear as dots or lines depending on the plane of section. The field is approximately 11 microns across.
description: B0001806 Nerve fibre in corneal stroma. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.15468/dl.ka9y7w
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Greece",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Loricifera",
 "Year 1000-2022"
 ]
}

 The dataset includes 18 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242083-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46dxr8
title: Occurrence Download

description: A dataset containing 2306575 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Greece",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2306575 records from 1565 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0182323-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60933/prdr/rwjucx
title: Lysine Deprivation Suppresses Adipogenesis in 3T3-L1 Cells: A Transcriptome Analysis

description: Organism: Mus musculus Summary: It has been reported that low concentration of lysine suppressed lipid accumulation and transcription of several adipogenic genes in 3T3-L1 preadipocytes, however, the detailed lysine deprivation-specific cellular transcriptomic changes and the altered pathways have not yet been fully decrypted. Overall design: Using 3T3-L1 cells, we performed RNA sequencing on undifferentiated cells, differentiated cells, and differentiated cells under a lysine-free culture medium
DOI: 10.60933/prdr/rwjucx/avyjd6
title: SRR23252441.sra

description: Treatment: Adipogenic differentiation
DOI: 10.15468/dl.d6u327
title: Occurrence Download

description: A dataset containing 17994 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is one of (Mollusca, Lissachatina fulica (Férussac, 1821))"
 ]
}

 The dataset includes 17994 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0256330-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ux99vx
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dicranomyia consimilis (Zetterstedt, 1838)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0219190-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.77cz9v
title: Occurrence Download

description: A dataset containing 53 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bulbostylis oligostachys (Hochst. ex A.Rich.) C.B.Clarke"
 ]
}

 The dataset includes 53 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0213203-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.77svac
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pistacia vera L.",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0194252-220831081235567/datasets/export for details.
DOI: 10.15468/dl.m495sq
title: Occurrence Download

description: A dataset containing 4582 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Begonia L."
 ]
}

 The dataset includes 4582 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0182330-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc4xn5v
title: CCDC 146697: Experimental Crystal Structure Determination

description: Related Article: A.Furstner, O.R.Thiel, N.Kindler, B.Bartkowska|2000|J.Org.Chem.|65|7990|doi:10.1021/jo0009999
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc4xn6w
title: CCDC 146698: Experimental Crystal Structure Determination

description: Related Article: A.Furstner, O.R.Thiel, N.Kindler, B.Bartkowska|2000|J.Org.Chem.|65|7990|doi:10.1021/jo0009999
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc45rkl
title: CCDC 124699: Experimental Crystal Structure Determination

description: Related Article: S.M.Draper, M.Delamesiere, E.Champeil, B.Twamley, J.J.Byrne, C.Long|1999|J.Organomet.Chem.|589|157|doi:10.1016/S0022-328X(99)00399-X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc45rlm
title: CCDC 124700: Experimental Crystal Structure Determination

description: Related Article: S.M.Draper, M.Delamesiere, E.Champeil, B.Twamley, J.J.Byrne, C.Long|1999|J.Organomet.Chem.|589|157|doi:10.1016/S0022-328X(99)00399-X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc45rmn
title: CCDC 124701: Experimental Crystal Structure Determination

description: Related Article: S.M.Draper, M.Delamesiere, E.Champeil, B.Twamley, J.J.Byrne, C.Long|1999|J.Organomet.Chem.|589|157|doi:10.1016/S0022-328X(99)00399-X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc45rnp
title: CCDC 124702: Experimental Crystal Structure Determination

description: Related Article: S.M.Draper, M.Delamesiere, E.Champeil, B.Twamley, J.J.Byrne, C.Long|1999|J.Organomet.Chem.|589|157|doi:10.1016/S0022-328X(99)00399-X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc45rpq
title: CCDC 124703: Experimental Crystal Structure Determination

description: Related Article: S.M.Draper, M.Delamesiere, E.Champeil, B.Twamley, J.J.Byrne, C.Long|1999|J.Organomet.Chem.|589|157|doi:10.1016/S0022-328X(99)00399-X
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cc5m856
title: CCDC 167467: Experimental Crystal Structure Determination

description: Related Article: N.T.Tran, M.Kawano, L.F.Dahl|2001|J.Chem.Soc.,Dalton Trans.||2731|doi:10.1039/b103547a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.