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349 results for “Scanning microscopy”
Mapping mineralogical heterogeneities at the nm-scale by scanning electron microscopy in modern Sardinian stromatolites: Deciphering the origin of their laminations
<p>These are the raw or processed data used for a paper published in Chemical Geology by Debrie et al. (2022), entitled "Mapping mineralogical heterogeneities at the nm-scale by scanning electron microscopy in modern Sardinian stromatolites: Deciphering the origin of their laminations", <a href="https://doi.org/10.1016/j.chemgeo.2022.121059">https://doi.org/10.1016/j.chemgeo.2022.121059</a></p> <p>The data content is summarized in the List_description_of_data.xlsx file</p>
Dataset of Scanning Tunneling Microscopy (STM) images of model surfaces for elementary steps in catalytic reactions
<p>STM images presented in the dataset were recorded by the STRAS research group using a Omicron Variable Temperature STM (VT-STM) microscope, in the TASC laboratory of the CNR-IOM in Trieste.</p> <p>This work has been done within the NFFA-DI project funded by the European Union – NextGenerationEU - Missione 4, “Istruzione e Ricerca” – Componente 2, “Dalla ricerca all'impresa” – Linea di investimento 3.1,“Fondo per la realizzazione di un sistema integrato di infrastrutture di ricerca e innovazione” – Azione 3.1.1, “Creazione di nuove IR o potenziamento di quelle esistenti che concorrono agli obiettivi di Eccellenza Scientifica di Horizon Europe e costituzione di reti”.</p>
Dataset of Scanning Tunneling Microscopy (STM) images of graphene on nickel
<p>STM images presented in the dataset were recorded by the STRAS research group using a Omicron Variable Temperature STM (VT-STM) microscope, in the TASC laboratory of the CNR-IOM in Trieste.</p> <p> </p>
Simulated calibration dataset for 4D scanning transmission electron microscopy
<p>4D-STEM data frequently requires a number of calibrations in order to make accurate measurement: for instance, in various cases, it can be essential to measure and correct for diffraction shifts, account for ellipticity in the diffraction patterns, or determine the rotational offset between the real and diffraction planes.</p> <p>We've prepared a simulated 4D-STEM dataset which includes diffraction shifting, elliptical distortion, and an r-space/k-space rotational offset. Two HDF5 files each include the simulated data for two different electron probes: a standard probe, using a circular probe-forming aperture, and a 'bullseye' probe, using a patterned aperture. Each HDF5 file contains the following data objects:</p> <p>(a) the 'experimental' 4D-STEM scan of a strained single-crystal gold nanoparticle (size: (100,84,250,250) )</p> <p>(b) a 4D-STEM scan of a calibration sample of polycrystalline gold (size: (100,84,250,250) )</p> <p>(c) a stack of diffraction images of the electron probe over vacuum (size: (250,250,20) )</p> <p>(d) a single image of the electron probe over the sample and far from focus, such that the CBED forms a shadow image (size: (512,512) )</p>
Fluorescent Confocal Laser Scanning Microscopy of White Blood Cells, Cancer Cell Line MCF7, and Mixtures of these Cells: A Model System for Circulating Tumor Cell Biomarker Evaluation V.1
<p>This is a confocal laser scanning microscopy data set of white blood cells (leukocytes), the cancer cell line MCF7, and mixtures of these cells acquired on a Zeiss LSM 780 microscope in the University of Colorado Anschutz Medical Campus Advanced Light Microscopy Core. Cells are fluorescently labeled for DNA with DAPI (Sigma D9542), lipids with Bodipy 495/503 (Thermo Fisher D3922), the filament protein cytokeratin (CK) with pan-cytokertain-alexa555 antibodies (Cell Signaling Technologies 3478S) and the surface membrane antigen CD45 with CD45-alexa647 antibodies (Biolegend 304020). Bodipy was excited with a continuous wave (CW) 488 nm laser, alexa555 was excited with CW 561 nm laser, and alexa647 was excited with a CW 633 nm laser. The acquiring instrument does not have a CW 405 nm source so DAPI was excited by two photon process using a Coherent Cameleon ultrafast pulsed laser tuned to 765 nm. The objective used was a Zeiss Plan-Apochromat 20x, 0.8 NA, air.</p> <p>The data consists of 4 channel 8x8 mosaic z-stacks. The Zeiss software performed stitching of the mosaics. These stitched data images are included and marked with _Stitched at the end. Those interested in performing the stitching themselves can do this with the raw data files (without the _Stitched). The jpeg images are processed from the stitched LSM images. The LSM files contain additional meta data on the experiment including power levels and acquisition settings.</p> <p>The _Stiched .lsm files will load in ImageJ (tested with V.1.49) as 4 channel 3 stack images.</p> <p>This data is a model system for evaluating the DNA/Lipids/CK/CD45 biomarker panel to identify circulating tumor cells (CTCs). The D- population of the model is the WBCs and the D+ population is the MCF7 cancer cell line. The amount of separation the biomarker panel plus analysis algorithm can produce between these populations (D+/D-) is an estimate the sensitivity and specificity of the biomarker panel plus algorithm to CTCs.</p> <p>Experiments generating the data were performed over the course of 15 days. Peripheral blood samples were collected from the Gynecological Tissue and Fluid Bank (COMIRB 07-0935 / COMIRB 05-1081) from consenting patients undergoing surgery at the University of Colorado Hospital. Blood samples were used the same day they were collected. Blood samples were collected from 3 patients with benign conditions, labeled WBBN#, and 3 patients with ovarian cancer, labeled WBCA#. We do not expect there to be any difference in the isolated white blood cells samples prepared from the cancer and benign patients. Samples were stored at room temperature until white blood cells were isolated. Mixed samples were prepared by passaging a MCF7 flask and mixing it with isolated white blood cells before fixation. A schedule showing the time duration between collection, processing and imaging is included as “experimental schedule.gif”.</p> <p>The MCF7 cancer cell line was a kind gift from Dr. Heide Ford. Genomic DNA was isolated from the MCF7 cell line after the experiment and sent for cell line authentication. The gDNA was a match to MCF7. The authentication report and data are included in this submission.</p> <p>CD45 antibodies were exhausted on day 7. New antibody was purchased and received on day 8. The day 7 images only has labels for DAPI and Bodipy. The samples prepared with the old antibodies on days 4 and 7 were relabeled and imaged with the new antibodies on days 14 and 15. This labeling was also done to confirm the pan-CK antibodies remained good since they are dim in the MCF7 cells imaged on days 12 and 13. The pan-CK on days 14 and 15 looks the same as it did on days 5 and 7 confirming the antibodies are good.</p> <p>Four of the filters containing cells were not sufficiently flat to be acquired with a 3 slice z-stack so a 5 slice z-stack was used. These files have been zipped to compress them under the 2 GB limit permitted by zenodo.org</p> <p>Further information on how these samples were prepared, processed, and analyzed can be found in our associated 2016 SPIE Photonics West BIOS conference proceeding titled, “Quantitative image cytometry measurements of lipids, DNA, CD45 and cytokeratin for circulating tumor cell identification in a model system”, http://dx.doi.org/10.1117/12.2222317.</p> <p>This work was supported by funding provided to the University of Colorado Cancer Center by the American Cancer Society and awarded as Institutional Research Grant Number 57-001-53, by funding provided by the Defense Advanced Research Projects Agency under grant number N66001-10-4035, and by funding provided by NIH/NCATS Colorado CTSI Grant Number TL1 TR001081. The University of Colorado Anschutz Medical Campus Advanced Light Microscopy Core is also supported in part by NIH/NCATS Colorado CTSI Grant Number UL1 TR001082. The funders had no role in the study design, data collection, analysis, or decision to publish.</p>
Shape, membrane morphology, and morphodynamic response of metabolically active human mitochondria revealed by scanning ion conductance microscopy
<p>This contains the hole data set as well as all analysed data for the paper published in Beilstein Journal of Nanotechnology "Shape, membrane morphology and morphodynamic response of metabolically active human mitochondria revealed by Scanning Ion Conductance Microscopy".</p> <p>Most of the images were taken with the SICM. These uncompressed tiff files can be read and processed with the Gwyddion software or other scanning probe image processing software.</p>
Field Emission Scanning Electron microscopy from Zr-Cu-Ag metallic glass coatings after antibacterial test with E.Coli
<p>Field Emission Scanning Electron Microscopy Figures from metallic glass (Zr-Cu-Ag) antibacterial coatings. Coatings have the name SP in their file name. The non-coated comparison is PBT. This is after the antibacterial test with <em>E.coli</em> after 24 hours. </p>
Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post Acquisition Data Processing, Visualisation, and Structural Characterisation
<p>Scanning transmission electron microscopy data related to paper "Scanning transmission electron microscopy data related to paper "Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post Acquisition Data Processing, Visualisation, and Structural Characterisation", <a href="https://doi.org/10.1017/S1431927620024307">https://doi.org/10.1017/S1431927620024307</a>.</p>
How to reveal metastable skyrmionic spin structures by spin-polarized scanning tunneling microscopy
<p>We predict the occurrence of metastable skyrmionic spin structures such as antiskyrmions and<br> higher-order skyrmions in ultra-thin transition-metal films at surfaces using Monte Carlo simulations<br> based on a spin Hamiltonian parametrized from density functional theory calculations.Weshow that<br> such spin structures will appear with a similar contrast in spin-polarized scanning tunneling<br> microscopy images. Both skyrmions and antiskyrmions display a circular shape for out-of-plane<br> magnetized tips and a two-lobe butterfly contrast for in-plane tips. An unambiguous distinction can<br> be achieved by rotating the tip magnetization direction without requiring the information of all<br> components of the magnetization.</p>
Cryo-4D-STEM datasets on cells and cellular organelles for demonstrating a dose-Efficient cryo-EM technique: tilt-Corrected Scanning Transmission Electron Microscopy
<p>This upload contains three 4D-STEM datasets in .raw format for demonstrating a dose-efficient cryo-EM technique for thick samples: tilt-corrected Scanning Transmission Electron Microscopy (tcBF-STEM). The dataset dimension is 128130256*256. Data were acquired on vitrified intact E.coli cells and isolated human cell organelles. This upload also contains the EFTEM images in .mrc acqired in the same ROI as the 4D-STEM dataset. </p> <p>It also contains analysis of the manuscript's Fig 3 and Ext. data fig 8. </p>
Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin
<p>In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for <em>Stenotrophomonas rhizophila</em> (B68), Cy3 for <em>Bacillus licheniformis</em> (B65), and FAM for <em>Microbacterium lacticum</em> (B30). C1 combination refers to a combination containing B68 and B30. </p> <p><span>Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7.</span></p> <p>Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions. </p> <p>Details of the oligonucleotide probes are given below:</p> <table> <tbody> <tr> <td> <p><strong><span>Name of the species</span></strong></p> </td> <td> <p><strong><span>Sequences</span></strong></p> </td> <td> <p><strong><span>Max. excitation</span></strong></p> </td> <td> <p><strong><span>Max. emission</span></strong></p> </td> <td> <p><strong><span>Fluorophores</span></strong></p> </td> </tr> <tr> <td> <p><em><span>S. rhizophila</span></em><span> B68<span> </span></span></p> </td> <td> <p><span>GGGCCTTTACCCCGCCA</span></p> </td> <td> <p><span>649 nm</span></p> </td> <td> <p><span>670 nm</span></p> </td> <td> <p><span>Cy5</span></p> </td> </tr> <tr> <td> <p><em><span>B. licheniformis</span></em><span> B65</span></p> </td> <td> <p><span>ACCGCCTGCGCGCGCTT</span></p> </td> <td> <p><span>550 nm</span></p> </td> <td> <p><span>570 nm</span></p> </td> <td> <p><span>Cy3</span></p> </td> </tr> <tr> <td> <p><em><span>M. lacticum</span></em><span> B30</span></p> </td> <td> <p><span>CCCCACCCTTTCGCTCC</span></p> </td> <td> <p><span>495 nm</span></p> </td> <td> <p><span>520 nm</span></p> </td> <td> <p><span>FAM</span></p> </td> </tr> </tbody> </table>
Figs 16–21 in Redescription of Strombidium coronatum (Leegaard, 1915) Kahl, 1932 (Ciliophora, Spirotricha) based on live observation, protargol impregnation, and scanning electron microscopy
Figs 16–21. Strombidium coronatum, Irish Sea specimens (16–18, scanning electron micrographs; 19–21, protargol impregnation, micrographs of several focal planes were stacked, using the computer program CombineZP from Alan Hadley). 16 – ventrolateral view; 17 – left lateral view showing uniquely shaped peristome, which is roughly triangular in outline and almost flat, extending in the sagittal plane. The extrusomes insert in short oblique rows anteriorly to the girdle kinety; note that some of them are just ejected (arrowhead); 18 – posterior cell portion showing the sharp, longitudinal ridges that have already been illustrated in the original description by Leegaard (1915); 19 – left lateral view of an early divider; 20 – dorsolateral view of an early divider; 21 – ventrolateral view. AP – apical protrusion, BM – buccal membranelles, CM – collar membranelles, DC – distended cell surface, EX – extrusome attachment sites, GK – girdle kinety, MA – macronucleus, OP – oral primordium, VK – ventral kinety. Scale bars: 40 µm (16), 20 µm (17, 19–21), and 10 µm (18).
Figs 11–22 in Palp sensory structures in adult caddisflies of the suborder Annulipalpia (Trichoptera): a scanning electron microscopy study
Figs 11–22. Palp sensilla of caddisflies of the suborder Annulipalpia: 11 – N. bimaculata female, long trichoid sensilla on lateral surface of the fifth maxillary palp segment; 12 – N. bimaculata female, short chaetoid sensillum on ventral surface of the fourth maxillary palp segment; 13 – Ch. marginata male, a group of long chaetoid sensilla on medial surface of the second maxillary palp segment; 14 – D. varians male, truncated chaetoid sensillum on
Figs 7–10 in Palp sensory structures in adult caddisflies of the suborder Annulipalpia (Trichoptera): a scanning electron microscopy study
Figs 7–10. Labial palps of P. apicalis (7–8) and N. bimaculata (9–10) females. 7 – first and second segments; 8, 9 – third segment; 10 – sensory field on the third segment. Abbreviations: chs-s – short chaetoid sensilla; lts – long trichoid sensilla; pes-f – flattened petaloid sensilla; sf – sensory field. Roman numerals represent segment numbers.
Figs 1–6 in Palp sensory structures in adult caddisflies of the suborder Annulipalpia (Trichoptera): a scanning electron microscopy study
Figs 1–6. Medial (1–5) and ventrolateral (6) surfaces of maxillary palp of D. robusta male (Hydropsychidae). 1 – first segment; 2 – second segment; 3 – third segment; 4 – sensory field of petaloid sensilla on the first segment; 5 – fourth segment; 6 – tip of the fifth segment. Abbreviations: cfs – campaniform sensilla; chs-l – long chaetoid sensilla; chs-s – short chaetoid sensilla; lts – long trichoid sensilla; pes-c – curved petaloid sensilla; sf – sensory field. Roman numerals represent segment numbers.
РИС. 4. Прикрепительный аппарат глохидиев Beringiana beringiana: A–C – внешний вид крючков; D – макрошипы. Масштабные линейки 10 мкм (A–C) и 5 мкм (D). СканируюЩаЯ ЭлектроннаЯ микроскопиЯ. FIG. 4. Hooks (A–C) and macrospines (D) of Beringiana beringiana glochidia. Scale bars 10 µm (A–C) и 5 µm (D). Scanning electron microscopy. in Первые данные о морфологии глохидиев двустворчатых моллюсков Beringiana beringiana (Bivalvia, Unionidae) оЗера Дальнее, Камчатка
РИС. 4. Прикрепительный аппарат глохидиев Beringiana beringiana: A–C – внешний вид крючков; D – макрошипы. Масштабные линейки 10 мкм (A–C) и 5 мкм (D). СканируюЩаЯ ЭлектроннаЯ микроскопиЯ. FIG. 4. Hooks (A–C) and macrospines (D) of Beringiana beringiana glochidia. Scale bars 10 µm (A–C) и 5 µm (D). Scanning electron microscopy.
РИС. 5. Поверхности створки глохидиЯ со скульптурой и порами: А – наруЖнаЯ; В –внутреннЯЯ. Масштабные линейки 10 мкм. СканируюЩаЯ ЭлектроннаЯ микроскопиЯ. FIG. 5. Valve surfaces with the sculpture and pores: A – exterior; B – interior. Scale bars 10 µm. Scanning electron microscopy. in Первые данные о морфологии глохидиев двустворчатых моллюсков Beringiana beringiana (Bivalvia, Unionidae) оЗера Дальнее, Камчатка
РИС. 5. Поверхности створки глохидиЯ со скульптурой и порами: А – наруЖнаЯ; В –внутреннЯЯ. Масштабные линейки 10 мкм. СканируюЩаЯ ЭлектроннаЯ микроскопиЯ. FIG. 5. Valve surfaces with the sculpture and pores: A – exterior; B – interior. Scale bars 10 µm. Scanning electron microscopy.
РИС. 3. Раковины Зрелых глохидиев Beringiana beringiana в раЗных ракурсах: А–С – Закрытые раковины, вид со стороны створки (А), вентрального угла (В) и лигамента (С); D–F – полностью открытые раковины, вид иЗнутри (D), снаруЖи (E) и боковых краев створок (F); G, H – приоткрытые раковины, стрелка укаЗывает на остатки волокон мускулаЗамыкателЯ. МасштабнаЯ линейка 100 мкм. СканируюЩаЯ ЭлектроннаЯ микроскопиЯ. FIG. 3. Mature glochidial shells of Beringiana beringiana from different angles of view: A–C – closed shells, view from the valve side (A), ventral angle (B), and ligament (C); D–F – open shells, interior view (D), exterior view (E), and from lateral margins of valves (F); G, H – ajar shells, the arrows indicate the remains of the adductor muscle fibers. Scale bar 100 µm. Scanning electron microscopy. in Первые данные о морфологии глохидиев двустворчатых моллюсков Beringiana beringiana (Bivalvia, Unionidae) оЗера Дальнее, Камчатка
РИС. 3. Раковины Зрелых глохидиев Beringiana beringiana в раЗных ракурсах: А–С – Закрытые раковины, вид со стороны створки (А), вентрального угла (В) и лигамента (С); D–F – полностью открытые раковины, вид иЗнутри (D), снаруЖи (E) и боковых краев створок (F); G, H – приоткрытые раковины, стрелка укаЗывает на остатки волокон мускулаЗамыкателЯ. МасштабнаЯ линейка 100 мкм. СканируюЩаЯ ЭлектроннаЯ микроскопиЯ. FIG. 3. Mature glochidial shells of Beringiana beringiana from different angles of view: A–C – closed shells, view from the valve side (A), ventral angle (B), and ligament (C); D–F – open shells, interior view (D), exterior view (E), and from lateral margins of valves (F); G, H – ajar shells, the arrows indicate the remains of the adductor muscle fibers. Scale bar 100 µm. Scanning electron microscopy.
The initial stages of Ag fluorination: a scanning tunneling microscopy investigation
<p>Low Temperature scanning tunneling microscopy images of Ag(100) and Ag(110) crystals exposed at room temperature for different amounts of time to a fluorine-rich atmosphere. The temperature used for acquiring the STM images is written within the title of the file. </p> <p>The calibration factors for the STM images are 1.12 in X and Y, 0.867 in Z. </p> <p>These STM data are the raw images of the results shown in the paper published in ArXiv with the doi number 10.48550/arXiv.2410.04858.</p>
Atrial Fibrillation Designation with Micro-Raman Spectroscopy and Scanning Acoustic Microscopy
<p>This repository was constructed tp provide the <strong>Raman Spectroscopy</strong> data and figure files related to the manuscript “Atrial Fibrillation Designation with Micro-Raman Spectroscopy and Scanning Acoustic Microscopy”. </p>
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