cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0dv1j4k
title: CIL:1006, 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: 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
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 1 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/j07w6b91
title: CIL:14969, Mus musculus, CNS interneuron, pyramidal cell, basket cell. In Cell Image Library

description: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) colabelled for the CB1 cannabinoid receptor. This image is from the pyramidal cell layer in hippocampal CA1. Multiple EGFP+ bipolar interneurons are present within the pyramidal cell layer and a mesh of EGFP+ fibers and CB1+ axons is present around the pyramidal cell bodies, consistent with basket cell synapses. EGFP+ cells are also present in the stratum oriens and stratum radiatum. CB1 was detected with the L15 antibody (K. Mackie).

Section (40 um) was imaged with a 32X, 0.4 NA Achroplan 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. See Davis and Puhl 2011 (Pubmed ID 21305052) for a detailed staining protocol. This image is part of a series characterizing EGFP expression from the 5HT3 promoter throughout the brain.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 568; EGFP
Data qualification: Raw
DOI: 10.6075/j0930s6g
title: CIL:7501, gallus gallus, erythrocyte. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: spread nucleus
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: negative staining; tungsten compound
Processing history: unprocessed raw data
description: A drop of a preparation of chicken erythrocyte nuclei was exposed to low ionic strength and centrifuged onto a formvar-carbon film, fixed with paraformaldehyde and negatively stained with sodium phosphotungstate. Images were recorded at 40KX and accelerating voltage of 1MeV at the University of Wisconsin HVEM facility.This image was taken with a specimen tilt of 45 degrees. A grouped image of the same field at a 55 degree tilt provides an oblique stereo view of a tangle of chromatin fibers extending from the dispersed nucleus.
DOI: 10.6075/j0zw1jj8
title: CIL:46023, Homo sapiens. In Cell Image Library

description: Plate 26544 - 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/j0319tj7
title: CIL:28775, Homo sapiens. In Cell Image Library

description: Spinning disk confocal time-lapse imaging of mitosis in asynchronous HeLa cells transfected with control, nontargeting siRNA oligonucleotides, or siRNA oligonucleotides targeting HsKNL2. Top, nontargeting siRNA oligonucleotides; bottom, siRNA oligonucleotides targeting HsKNL2. DIC is shown on the left, and YFP-CENP-A is shown on the right. The control cell on the left begins in metaphase and, over the course of the video, completes mitosis successfully. Paired YFP-CENP-A loci oscillate during metaphase and then segregate to opposite poles during anaphase. In the HsKNL2 knockdown cells, YFP-CENP-A is not seen to localize at any point during the video. Two cells begin in metaphase and leave mitosis during the video. The DIC channel shows that chromosomes do not oscillate as seen in controls and, during anaphase, segregate with aberrant poleward movement in the cell on the left and nominal poleward movement in the cell on the right. The video is ∼75 min long, and the frame is ∼40 µm top to bottom. Images were acquired at 60-s intervals).
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal 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
Visualization methods: EYFP; visualization of contiguous regions
Processing history: unprocessed raw data
description: Images were acquired via a spinning disk confocal microscope (CSU10; McBain Instruments) mounted on an inverted microscope (TE2000e; Nikon). Strain TH32 coexpressing GFP-histone H2b and GFP–γ-tubulin was imaged using a 60× 1.4 NA plan Apo objective with 1.5× auxiliary magnification and a cooled CCD camera (Orca ER; Hamamatsu) binning 2 × 2. Strain OD31 expressing GFP–KNL-2 was imaged in the same manner without the 1.5× auxiliary magnification.
DOI: 10.15468/dl.qf3x3w
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Baccharoides anthelmintica"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009196-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17617/3.8fobm8
title: Datasets of "Direct to indirect band gap transition induced by approximately dark states"

description: The dataset contains raw data files of the ARPES and data files of the DFT bandstructure calculations.
DOI: 10.15468/dl.j2u3p5
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Eragrostis autumnalis"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009199-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zy9t23
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Asparagus trichophyllus"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009198-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0cr5scs
title: CIL:8472, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.5281/zenodo.17489750
title: A Comparative Review of Celiac Disease and Malabsorption Across Clinical and Educational Sources

description: Celiac disease is an autoimmune disorder triggered by gluten in genetically susceptible individuals, resulting in small intestinal mucosal damage and impaired nutrient absorption. This review analyzes five authoritative sources—Cleveland Clinic, NHS, Mayo Clinic, MSD Manual (Professional Edition), and a PubMed Central review (PMC1435993)—examining their approaches to patient education, clinical guidance, and scientific explanation. Patient-focused sources emphasize symptom recognition, dietary management, and prevention of complications, while professional references highlight diagnostic criteria, pathophysiology, and evidence-based management strategies. Integrating these perspectives underscores the importance of early diagnosis, lifelong adherence to a gluten-free diet, and comprehensive patient education in improving outcomes.
DOI: 10.5281/zenodo.17489751
title: A Comparative Review of Celiac Disease and Malabsorption Across Clinical and Educational Sources

description: Celiac disease is an autoimmune disorder triggered by gluten in genetically susceptible individuals, resulting in small intestinal mucosal damage and impaired nutrient absorption. This review analyzes five authoritative sources—Cleveland Clinic, NHS, Mayo Clinic, MSD Manual (Professional Edition), and a PubMed Central review (PMC1435993)—examining their approaches to patient education, clinical guidance, and scientific explanation. Patient-focused sources emphasize symptom recognition, dietary management, and prevention of complications, while professional references highlight diagnostic criteria, pathophysiology, and evidence-based management strategies. Integrating these perspectives underscores the importance of early diagnosis, lifelong adherence to a gluten-free diet, and comprehensive patient education in improving outcomes.
DOI: 10.6075/j0v40t66
title: CIL:8474, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.15468/dl.pfcrym
title: Occurrence Download

description: A dataset containing 34277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Micromys minutus"
 ]
}

 The dataset includes 34277 records from 472 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009200-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g3axks
title: Occurrence Download

description: A dataset containing 3199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "SpeciesKey is one of (Agasicles hygrophila, Chrysolina, Chrysolina quadrigemina, Chrysolina hyperici, Colaspis, Neogalerucella calmariensis, Neogalerucella pusilla, Neolema, Oberea shirahatai, Nanophyes marmoratus, Cleopus japonicus, Grypus equiseti, Cotesia urabae, Pauesia nigrovaria, Microctonus aethiopoides, Eriborus, Tetramesa romana, Pseudaphycus maculipennis, Euplectrus, Thripobius semiluteus, Tamarixia triozae, Trichilogaster acaciaelongifoliae, Cheilosia psilophthalma, Volucella inanis, Volucella inanis, Phytomyza vitalbae, Macrolabis pilosellae, Procecidochares alani, Lathronympha strigana, Cydia succedana, Cochylis atricapitana, Agonopterix, Agonopterix alstroemeriana, Agonopterix assimilella, Oxyptilus pilosellae, Chamaesphecia mysiniformis, Arytainilla spartiophila, Rhizaspidiotus donacis, Tetranychus lintearius, Entyloma ageratinae, Melampsora hypericorum, Puccinia myrsiphylli, Prospodium tuberculatum, Prospodium tuberculatum, Sclerotinia sclerotiorum, Puccinia hieracii, Puccinia berberidis-darwinii, Uromyces pencanus, Uromyces pencanus, Exapion ulicis, Trichosirocalus horridus, Rhinocyllus conicus, Sericothrips staphylinus, Gonioctena olivacea, Lochmaea suturalis, Lema cyanella, Aphthona nonstriata, Ceratapion onopordi, Monophadnus spinolae, Trissolcus japonicus, Cheilosia urbana, Pempelia genistella, Platyptilia isodactylus, Aceria vitalbae, Dolichogenidea eucalypti, Freudeita, Blaptea, Cassida rubiginosa, Cassida rubiginosa, Longitarsus jacobaeae, Hylobius transversovittatus, Urophora stylata, Urophora solstitialis, Urophora cardui, Tyria jacobaeae, Phoma clematidina, Metoecus paradoxus, Metoecus paradoxus, Wheeleria spilodactylus, Phoma exigua exigua, Puccinia lantanae, Puccinia lantanae, Puccinia araujae, Gargaphia decoris, Leptoypha hospita, Leptoypha hospita, Leptoypha hospita, Leptoypha hospita, Leucoptera spartifoliella, Hydrellia egeriae, Polypedilum tuburcinatum, Lema basicostata, Puccinia suaveolens, Anthonomus kuscheli, Anthonomus kuscheli)",
 "Year 2010-2025"
 ]
}

 The dataset includes 3199 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009201-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0xk8fm5
title: CIL:6183, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.
DOI: 10.6075/j0jh3jr6
title: CIL:47653, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Vcam1)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
DOI: 10.6075/j0sn07kn
title: CIL:47652, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Vcam1)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
DOI: 10.6075/j0dv1hh3
title: CIL:47651, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Vcam1)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.