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238 results for “Molecular Imaging”
Dataset of "Neutron imaging and molecular simulation of systems from methane and p‑xylene"
<p>The dataset contains parameterizations, and input files for molecular dynamics simulations used in the study of methane dissolution in p-xylene. For selected conditions, full simulation data, i.e., trajectories and energetics are provided. All used simulation results data are provided in the table, along with the measured experimental data.</p>
Cryo-OrbiSIMS for 3D molecular imaging of a bacterial biofilm in its native state
<p>We developed a method for analysis and imaging of biological samples in their native state, by combining a cryo-OrbiSIMS instrument with cryogenic sample handling and high-pressure freezing. By using this method, we did analysis and imaging of frozen-hydrated mature <em>Pseudomonas aeruginosa</em> biofilm, which allows the identification and map of quorum sensing signaling molecules, nucleobases and bacterial membrane molecules with high spatial-resolution and high mass-resolution. Some of quorum sensing signaling molecules were further confirmed by MS/MS. By comparing the analysis of frozen-hydrated <em>Pseudomonas aeruginosa</em> biofilm with the freeze-dried one, we dicover that signal intensity of all interesting molecules get enhanced in the frozen-hydrated state. Especially for polar molecules, such as amino acid, it could even achieve 10,000 fold increasing. Here, we provide the original OrbiSIMS data including MS and MS/MS spectra, depth profile and images of frozen-hydrated and freeze-dried <em>Pseudomonas aeruginosa</em> biofilm. The data could be open by using SurfaceLab Version 7.0 (ION-TOF, Germany).</p>
Reference data and analysis software for "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane"
<p>Reference data set for the single molecule co-tracking analysis presented in "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane". Corresponding author for further inquiries:</p> <p>Prof. Dr. Jacob Piehler</p> <p>University of Osnabrück, Department of Biology/Chemistry, Division of Biophysics, Barbarastr. 11, 49076 Osnabrück, Germany</p> <p>https://www.biophysik.uni-osnabrueck.de/</p>
◂Fig.15 Scanning electron micrographs (SEM) showing transverse rows of dentition on Dinaride Zospeum and Iberozospeum radulae; (a) Z. pretneri, (NMBE 553290), Gornja Cerovačka pećina, Croatia, transverse rows of teeth on long, slender basal plates (bp), rachidian (r) and lateral teeth (l), arrows indicate medial grooves on mesocones of individual teeth; (b) Z. isselianum, NMBE 553389, Turjeva jama, Slovenia, ibid.; (c) Iberozospeum sp. (RMNH.MOL.234,116), Cueva a Sul, straight transverse rows of small, seemingly bi-cuspid lateral teeth (l) with reduced mesocones on compact basal plates; (d) ibid., close up view of rachidian teeth (r), lateral fang-like teeth (l) and transitional teeth (t); (e) I. vasconicum, (AJC 1848), Cueva Ermita de Sandaili, rachidian teeth (r) flanked by 4-cuspid lateral teeth (l), C. ibazoricum-like in form; (f) Iberozospeum sp. (RMNH. MOL.234108), Cueva la Torcona, lateral teeth showing reduced mesocones (me) flanked by long, fang-like endo- and ectocones (e), rachidian tooth (r) (flipped over in upper righthand corner of image); (g) I. zaldivarae (AJC 1876a), Cueva de Las Paúles, transverse rows of teeth showing varying cusp lengths; (h) ibid., close up view (left to right) of marginal (m) and transitional teeth (t) on short, compact basal plates (bp). — Magnification varies for each perspective, see scale bars; all Figs taken by M. Ruppel, (ret.) Goethe University Frankfurt am Main in Molecular investigation and description of Iberozospeum n. gen., including the description of one new species (Eupulmonata, Ellobioidea, Carychiidae)
◂Fig.15 Scanning electron micrographs (SEM) showing transverse rows of dentition on Dinaride Zospeum and Iberozospeum radulae; (a) Z. pretneri, (NMBE 553290), Gornja Cerovačka pećina, Croatia, transverse rows of teeth on long, slender basal plates (bp), rachidian (r) and lateral teeth (l), arrows indicate medial grooves on mesocones of individual teeth; (b) Z. isselianum, NMBE 553389, Turjeva jama, Slovenia, ibid.; (c) Iberozospeum sp. (RMNH.MOL.234,116), Cueva a Sul, straight transverse rows of small, seemingly bi-cuspid lateral teeth (l) with reduced mesocones on compact basal plates; (d) ibid., close up view of rachidian teeth (r), lateral fang-like teeth (l) and transitional teeth (t); (e) I. vasconicum, (AJC 1848), Cueva Ermita de Sandaili, rachidian teeth (r) flanked by 4-cuspid lateral teeth (l), C. ibazoricum-like in form; (f) Iberozospeum sp. (RMNH. MOL.234108), Cueva la Torcona, lateral teeth showing reduced mesocones (me) flanked by long, fang-like endo- and ectocones (e), rachidian tooth (r) (flipped over in upper righthand corner of image); (g) I. zaldivarae (AJC 1876a), Cueva de Las Paúles, transverse rows of teeth showing varying cusp lengths; (h) ibid., close up view (left to right) of marginal (m) and transitional teeth (t) on short, compact basal plates (bp). — Magnification varies for each perspective, see scale bars; all Figs taken by M. Ruppel, (ret.) Goethe University Frankfurt am Main
◂Fig. 13 Crystallographic structure on the columellar lamellae of Dinaride Zospeum and Iberozospeum shells; (a) Zospeum spelaeum, (AJC 847), Betalov Spodmol jama, Slovenia (45.7922 14.1877), pattern of low, non-overlapping, wedges of crystallographic structure on the lamella; (b) Zospeum spelaeum, (MCBI CSR SASA 37049a), Velika Pasica, Slovenia (N45.9189 E14.4934), non-overlapping wedges of crystallographic structure on lamella in old shell; (c) Iberozospeum sp., (RMNH.MOL. 234,120), Cueva Refugio, Trucios, overview of dense, overlapping, scale-like wedges of localized, crystallographic structure on upper part of the lower lamella; (d) ibid., closeup view of c; (e) Iberozospeum sp., (RMNH.MOL. 234,104), Cueva del Comediante, Santander, upper part of the lamella of chemically treated shell showing dense, overlapping wedges of localized, crystallographic structure; (f) Iberozospeum sp., (RMNH. MOL. 234,141), Cueva a Sul, Oviedo, localized, overlapping wedges of crystallographic structure on lamella of chemically treated shell; (g) Iberozospeum vasconicum, (AJC 1849), Cueva Arrikrutz, overview of dense, localized, crystallographic structure on lower part of the lamella; h, ibid., closeup view of g. — Magnification varies for each perspective, see scale bars; Figs. a–b, g–h) imaged by M. Ruppel, (ret.) Goethe University Frankfurt am Main; Figs. c–f imaged by Dirk Vendermarel, Naturalis Biodiversity Center in Molecular investigation and description of Iberozospeum n. gen., including the description of one new species (Eupulmonata, Ellobioidea, Carychiidae)
◂Fig. 13 Crystallographic structure on the columellar lamellae of Dinaride Zospeum and Iberozospeum shells; (a) Zospeum spelaeum, (AJC 847), Betalov Spodmol jama, Slovenia (45.7922 14.1877), pattern of low, non-overlapping, wedges of crystallographic structure on the lamella; (b) Zospeum spelaeum, (MCBI CSR SASA 37049a), Velika Pasica, Slovenia (N45.9189 E14.4934), non-overlapping wedges of crystallographic structure on lamella in old shell; (c) Iberozospeum sp., (RMNH.MOL. 234,120), Cueva Refugio, Trucios, overview of dense, overlapping, scale-like wedges of localized, crystallographic structure on upper part of the lower lamella; (d) ibid., closeup view of c; (e) Iberozospeum sp., (RMNH.MOL. 234,104), Cueva del Comediante, Santander, upper part of the lamella of chemically treated shell showing dense, overlapping wedges of localized, crystallographic structure; (f) Iberozospeum sp., (RMNH. MOL. 234,141), Cueva a Sul, Oviedo, localized, overlapping wedges of crystallographic structure on lamella of chemically treated shell; (g) Iberozospeum vasconicum, (AJC 1849), Cueva Arrikrutz, overview of dense, localized, crystallographic structure on lower part of the lamella; h, ibid., closeup view of g. — Magnification varies for each perspective, see scale bars; Figs. a–b, g–h) imaged by M. Ruppel, (ret.) Goethe University Frankfurt am Main; Figs. c–f imaged by Dirk Vendermarel, Naturalis Biodiversity Center
◂Fig. 14 Scanning electron micrographs (SEM) showing radular ribbon form, middle adhesive zone (az) and rows of dentition (rd) of Dinaride and Iberian individuals (notation denotes aspects on one Dinaride Zospeum and one Iberozospeum ribbon); (a) Z. exiguum (NMBE 553384), Križna jama, Slovenia (45.7452, 14.4673), long and narrow, tapered anterior end (tae), short adhesive zone (az), bottom furled with narrow obtuse or straight base (nosb); (b) Z. pretneri, (NMBE 553290), Gornja Cerovačka pećina, Croatia (44.2701, 15.8855), ibid., with straight base; (c) I. vasconicum, (AJC 1848), Cueva Ermita de Sandaili (42.9994, -2.4381), moderately long and broad, tapered anterior end (tae), prominent adhesive zone (az), straight base (sb); (d) I. zaldivarae, (AJC 1876), Cueva de Las Paúles (43.1282, -2.7362), ibid.; (e) Iberozospeum sp. (RMNH.MOL. 234,109), Cueva de la Foz, long and broad, ibid; (f) Iberozospeum sp., (RMNH.MOL. 234,144), Cueva de Rales, very long and broad, ibid; (g) Iberozospeum sp., (RMNH.MOL. 234,116), Cueva a Sul, long and broad, ibid; (h) Iberozospeum sp., (RMNH.MOL. 234,108), Cueva de Torcona, very long and broad, ibid. — Magnification varies for each perspective, see scale bars; all Figs imaged by M. Ruppel, (ret.) Goethe University Frankfurt am Main in Molecular investigation and description of Iberozospeum n. gen., including the description of one new species (Eupulmonata, Ellobioidea, Carychiidae)
◂Fig. 14 Scanning electron micrographs (SEM) showing radular ribbon form, middle adhesive zone (az) and rows of dentition (rd) of Dinaride and Iberian individuals (notation denotes aspects on one Dinaride Zospeum and one Iberozospeum ribbon); (a) Z. exiguum (NMBE 553384), Križna jama, Slovenia (45.7452, 14.4673), long and narrow, tapered anterior end (tae), short adhesive zone (az), bottom furled with narrow obtuse or straight base (nosb); (b) Z. pretneri, (NMBE 553290), Gornja Cerovačka pećina, Croatia (44.2701, 15.8855), ibid., with straight base; (c) I. vasconicum, (AJC 1848), Cueva Ermita de Sandaili (42.9994, -2.4381), moderately long and broad, tapered anterior end (tae), prominent adhesive zone (az), straight base (sb); (d) I. zaldivarae, (AJC 1876), Cueva de Las Paúles (43.1282, -2.7362), ibid.; (e) Iberozospeum sp. (RMNH.MOL. 234,109), Cueva de la Foz, long and broad, ibid; (f) Iberozospeum sp., (RMNH.MOL. 234,144), Cueva de Rales, very long and broad, ibid; (g) Iberozospeum sp., (RMNH.MOL. 234,116), Cueva a Sul, long and broad, ibid; (h) Iberozospeum sp., (RMNH.MOL. 234,108), Cueva de Torcona, very long and broad, ibid. — Magnification varies for each perspective, see scale bars; all Figs imaged by M. Ruppel, (ret.) Goethe University Frankfurt am Main
Partitioned Image Data for Machine Learning Analysis of Molecular Biology Figures
<p><strong> Corpus Composition</strong></p> <p>This data collection provides four types of hand-curated images from open access research articles images. The types are:</p> <ol> <li>chart (n=811): data displays such as bar charts, scatterplots, line graphs, etc.</li> <li>diagram (n=816): any general conceptual diagram</li> <li>gel (n=1182): the output of electrophoresis experiments in Northern, Western, or Southern Blot experiments. </li> <li>histology (n=3458): microscope images of tissue with histological staining</li> </ol> <p>The images are simply organized in subdirectories as individual files. File names are based on PubMed Id and Figure number. </p>
Image segmentation masks for curved arrows on molecular images from chemical reaction mechanism images
<p>The dataset presented herein is designed as a ground truth for image segmentation tasks focused on noise extraction in Optical Chemical Structure Recognition (OCSR) processes. It comprises 73 manually extracted and annotated images from real reaction mechanism images, along with 5320 synthetic molecular images generated using RDKit, each featuring computer-drawn curved arrows on random locations on the molecular image pertinent to their respective tasks. Curved arrows are prevalent in chemical reaction mechanism images and significantly impact the accuracy of molecular identity recognition. This dataset aims to enhance OCSR tasks by enabling the pretreatment of molecular images to remove noise, thereby improving molecular recognition accuracy.</p>
Ultrafast imaging of molecular chirality with photoelectron vortices
<p>This is the plotting data and plotting scripts for the publication: <strong>“Ultrafast imaging of molecular chirality with photoelectron vortices”. </strong>Preprint available at: https://arxiv.org/abs/2202.07289. A readme.txt file is included with the data.</p> <p><strong>Authors:</strong><br> Xavier Barcons Planas, Andrés Ordóñez, Maciej Lewenstein, Andrew Stephen Maxwell</p> <p><strong>Abstract:</strong></p> <p>Ultrafast imaging of molecular chirality is a key step towards the dream of imaging and interpreting electronic dynamics in complex and biologically relevant molecules. Here, we propose a new ultrafast chiral phenomenon exploiting recent advances in electron optics allowing access to the orbital angular momentum of free electrons. We show that strong-field ionization of a chiral target with a few-cycle linearly polarized 800 nm laser pulse yields photoelectron vortices, whose chirality reveals that <br> of the target, and we discuss the mechanism underlying this phenomenon. Our work opens new perspectives in recollision-based chiral imaging.</p>
SMiCRM: A Benchmark Dataset of Mechanistic Molecular Images
<p>Optical chemical structure recognition (OCSR) systems aim to extract the molecular structure information, usually in the form of molecular graph or SMILES, from images of chemical molecules. While many tools have been developed for this purpose, challenges still exist due to different types of noises that might exist in the images. Specifically, we focus on the “arrow-pushing” diagrams, a typical type of chemical images to demonstrate electron flow in mechanistic steps. We present Structural molecular identifier of Molecular images in Chemical Reaction Mechanisms (SMiCRM), a dataset designed to benchmark machine recognition capabilities of chemical molecules with arrow-pushing annotations. Comprising 453 images, it spans a broad array of organic chemical reactions, each illustrated with molecular structures and mechanistic arrows. SMiCRM offers a rich collection of annotated molecule images for enhancing the benchmarking process for OCSR methods. This dataset includes a machine-readable molecular identity for each image as well as mechanistic arrows showing electron flow during chemical reactions. It presents a more authentic and challenging task for testing molecular recognition technologies, and achieving this task can greatly enrich the mechanisitic information in computer-extracted chemical reaction data.</p>
VLA C-band continuum images of the Central Molecular Zone
<p><strong>VLA C-band continuum images of the Central Molecular Zone</strong></p> <p><strong>The affiliated publication is Lu et al. 2019, ApJS, 244, 35. Please consider to cite it if you use images in this repository.<br> The ADS link is: https://ui.adsabs.harvard.edu/abs/2019ApJS..244...35L/abstract</strong></p> <p><strong>There are four tiles:</strong></p> <ul> <li>Sgr B2</li> <li>Dust Ridge</li> <li>Sgr A</li> <li>Sgr C</li> </ul> <p><strong>For each tile, there are six images</strong> (the PB correction is not by directly dividing the images by PB. The CASA task widebandpbcor is used to perform wideband PB correction)</p> <ul> <li>*_CONT_tclean_nterm2.alpha.fits: PB-uncorrected spectral index.</li> <li>*_CONT_tclean_nterm2.image.tt0.fits: PB-uncorrected image.</li> <li>*_CONT_tclean_nterm2.pb.tt0.fits: Primary beam.</li> <li>*_CONT_tclean_nterm2.pbcor.image.alpha.error.fits: PB-corrected spectral index uncertainty.</li> <li>*_CONT_tclean_nterm2.pbcor.image.alpha.fits: PB-corrected spectral index.</li> <li>*_CONT_tclean_nterm2.pbcor.image.tt0.fits: PB-corrected image.</li> </ul>
SI_III_4_Spatialized metabolomic annotation combining MALDI imaging and molecular network
<p>Ces documents regroupent les données supplémentaires générés lors du développement méthdologique pour la création de réseaux moléculaires par MALDI-FT-ICR IMS. Un .ppt regroupe l'ensemble des cartographies ioniques spécifiques à chaque ion.</p>
Molecular Breast Imaging as a Screening Tool for Women With Dense Breasts
ClinicalTrials.gov study NCT00620373. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Prospective Evaluation of Immunological, Molecular-genetic, Image-based and Microbial Analyzes to Characterize Tumor Response and Control in Patients With Inoperable Stage III NSCLC Treated With Chemo
ClinicalTrials.gov study NCT05027165. IPD Sharing: NO. Countries: 1. Publications: 1.
Low Dose Molecular Breast Imaging as a Screening Tool for Women With Dense Breasts
ClinicalTrials.gov study NCT01925170. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Molecular and Whole-body MR Imaging in Lymphomas
ClinicalTrials.gov study NCT02389101. IPD Sharing: NO. Countries: 1. Publications: 12.
Data from: Salty Sensors, Fresh Ideas: The use of molecular and imaging sensors in understanding plankton dynamics across marine and freshwater ecosystems
Open the record for dataset details and reuse information.
An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization
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Data for: PIEZO1-HaloTag hiPSCs: bridging molecular, cellular and tissue imaging
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FIGURES 5–8. Type specimen and molecular voucher images. 5 in A New Monotypic Genus from the American Southwest to accommodate "Semiothisa" kuschea (Geometridae: Ennominae)
FIGURES 5–8. Type specimen and molecular voucher images. 5, HOLOTYPE male of Semiothisa kuschea, and 6, label data (image credit Chris Grinter); 7, voucher image of "Isochromodes" "infida" (GB-CR-1241), sister taxon of Metrica misidentified as Certima dositheata in Murillo-Ramos et al. (2019) and Brehm et al. (2019) (image taken from, and image credit to, Supplement File 5 of Brehm et al. (2019)); 8, SYNTYPES of Sabulodes infida from USNM type search (https://collections.USNM.si.edu/ search/ento/). Images not to scale.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.