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30 results for “Atomic Force Microscopy”
Atomic force microscopy indentation data of zebrafish spinal cord sections
<p>The HDF5 file was created using the Python package nanite. It contains 1132 raw atomic force microscopy (AFM) force-indentation curves of zebrafish spinal cord sections, the preprocessed curves, and the corresponding fits to the approach part. In addition, a manual rating was assigned to each force-indentation curve. The intended use of this dataset is the application of machine-learning approaches to quantify AFM data quality for biological tissues.</p>
Mechanical characterisation of the developing cell wall layers of tension wood fibres by Atomic Force Microscopy
<p>This dataset corresponds to the Arnould et al. (2022) paper (available at https://www.biorxiv.org/content/10.1101/2021.09.23.461481v1.full) on the mechanical characterization of developing cell wall layers of tension wood fibers by Atomic Force Microscopy. It contains all raw AFM files (Bruker format .spm, readable by the free software Gwyddion for example) corresponding to mechanical measurements of poplar reaction wood cells (clone 717-1B4) along 3 radial lines/rows, starting from the cambium. Each cell is identified by its "macroscopic" distance from the cambium (value in µm in the name of each file corresponding to the displacement of the sample in the AFM) which was corrected after using the AFM optical image captures. Some files, with a -z extension after the distance value, correspond to a zoom into the cell wall. The data also contain measurements made for mechanical calibration on epoxy embedded Kevlar fibers, controlled measurements in the embedding resin between each radial line and measurements in normal wood cells. Two csv files containing final data extracted from AFM measurements that give the value of the indentation modulus and the relative thickness to cell diameter ratio (by AFM and by phase contrast optical microscopy) in each cell wall layer as a function of cambium distance are also provided.</p>
Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation: Confocal and atomic force microscopy
<p><strong>Summary</strong></p> <p>Dataset of imaging data related to the publication Raudenska, M., Kratochvilova, M., Vicar, T., Gumulec, J., Balvan, J., Polanska, H. Pribyl, J. & Masarik, M.:Cisplatin enhances cell stiffness and decreases invasiveness rate in prostate cancer cells by actin accumulation. <em>Scientific Reports </em><strong>2019, </strong>9, 1660</p> <p>This dataset includes image data of <em>atomic force microcopy</em> (Young modulus) and <em>confocal microscopy</em>(staining of F-actin and β-tubulin) of prostate cell lines PNT1A, 22Rv1, and PC-3. </p> <p><strong>Materials and Methods</strong></p> <p><em>Cells, cell culture conditions</em></p> <p>Cells confluent up to 50–60% were washed with a FBS-free medium and treated with a fresh medium with FBS and required antineoplastic drug concentration (IC50 concentration for the particular cell line). The cells were treated with 93 µM (PC-3), 38 µM (PNT1A), and 24 µM (22Rv1) of cisplatin (Sigma-Aldrich, St. Louis, Missouri), respectively. IC50 concentrations used for treatment with docetaxel (Sigma-Aldrich, St. Louis, Missouri) were 200nM for PC-3, 70nM for PNT1A, and 150nM for 22Rv1. </p> <p><em>Long-term zinc (II) treatment of cell cultures</em></p> <p>Cells were cultivated in the constant presence of zinc(II) ions. Concentrations of zinc(II) sulphate in the medium were increased gradually by small changes of 25 or 50 µM. The cells were cultivated at each concentration no less than one week before harvesting and their viability was checked before adding more zinc. This process was used to select zinc resistant cells naturally and to ensure better accumulation of zinc within the cells (accumulation of zinc is usually poor during the short-term treatment of prostate cancer cells). Total time of the cultivation of cell lines in the zinc(II)-containing media exceeded one year. Resulting concentrations of zinc(II) in the media (IC50 for the particular cell line) were 50 µM for the PC-3 cell line, 150 µM for the PNT1A cell line, and 400 µM for the 22Rv1 cell line. The concentrations of zinc(II) in the media and FBS were taken into account. </p> <p><em>Actin and tubulin staining</em></p> <p>β-tubulin was labeled with anti- β tubulin antibody [EPR1330] (ab108342) at a working dilution of 1/300. The secondary antibody used was Alexa Fluor® 555 donkey anti-rabbit (ab150074) at a dilution of 1/1000. Actin was labeled with Alexa Fluor™ 488 Phalloidin (A12379, Invitrogen); 1 unit per slide. For mounting Duolink® In Situ Mounting Medium with DAPI (DUO82040) was used. The cells were fixed in 3.7% paraformaldehyde and permeabilized using 0.1% Triton X-100. </p> <p><em>Confocal microscopy</em></p> <p>The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm.</p> <p><em>Atomic force microscopy</em></p> <p>We used the bioAFM microscope JPK NanoWizard 3 (JPK, Berlin, Germany) placed on the inverted optical microscope Olympus IX‑81 (Olympus, Tokyo, Japan) equipped with the fluorescence and confocal module, thus allowing a combined experiment (AFM‑optical combined images). The maximal scanning range of the AFM microscope in X‑Y‑Z range was 100‑100‑15 µm. The typical approach/retract settings were identical with a 15 μm extend/retract length, Setpoint value of 1 nN, a pixel rate of 2048 Hz and a speed of 30 µm/s. The system operated under closed-loop control. After reaching the selected contact force, the cantilever was retracted. The retraction length of 15 μm was sufficient to overcome any adhesion between the tip and the sample and to make sure that the cantilever had been completely retracted from the sample surface. Force‑distance (FD) curve was recorded at each point of the cantilever approach/retract movement. AFM measurements were obtained at 37°C (Petri dish heater, JPK) with force measurements recorded at a pulling speed of 30 µm/s (extension time 0.5 sec).</p> <p>The Young's modulus (E) was calculated by fitting the Hertzian‑Sneddon model on the FD curves measured as force maps (64x64 points) of the region containing either a single cell or multiple cells. JPK data evaluation software was used for the batch processing of measured data. The adjustment of the cantilever position above the sample was carried out under the microscope by controlling the position of the AFM‑head by motorized stage equipped with Petri dish heater (JPK) allowing precise positioning of the sample together with a constant elevated temperature of the sample for the whole period of the experiment. Soft uncoated AFM probes HYDRA-2R-100N (Applied NanoStructures, Mountain View, CA, USA), i.e. silicon nitride cantilevers with silicon tips are used for stiffness studies because they are maximally gentle to living cells (not causing mechanical stimulation). Moreover, as compared with coated cantilevers, these probes are very stable under elevated temperatures in liquids – thus allowing long-time measurements without nonspecific changes in the measured signal.</p> <p><em>Image analysis</em></p> <p>Fluorescence microscopy data were analyzed in ImageJ 1.52h and Python 3.7.1 as follows: cells were manually segmented using actin fluorescence channel, two regions were created for analysis: whole cell and cell periphery, lining a 4 μm thick region around cell border and including most of periphery actin cytoskeleton. In these two regions following parameters were measured for both actin and tubulin fluorescence: Integrated intensity, median intensity, and following regions were measured to describe cell morphology: Cell area, Maximum caliper (max feret diameter), roundness, and aspect ratio. Moreover, stress fibers were manually segmented in every cell and following parameters were measured: number of fibers per cell, feret angle of fiber, integrated intensity, fiber length, mean intensity. Next, a standard deviation of feret angles of individual fibers was calculated relatively to mean of feret angle using a circstd function from scipy package for Python.</p> <p><strong>Identification of files</strong></p> <p><em>Microscopy data</em></p> <p>Files are separated into individual zip files. The dataset of <em>confocal microscopy </em>is separated based on treatments: untreated control, docetaxel-treated cells, cisplatin-treated cells, zinc-treated cells. Filenames actin_tubulin_Zstack_cisplatin.zip, actin_tubulin_Zstack_untreated_control.zip, actin_tubulin_Zstack_zinc.zip, actin_tubulin_Zstack_docetaxel.zip. Files included in these ZIP archives are named as follows: "cellline_treatment_FOV". Files are 3-layer 16bit tiff files with layer sequence as follows: F-Actin (Phalloidin)/b-tubulin/Hoechst 33342. The dataset contains 242 FOVs of three cell line types/three treatments + one control, files are Z-stacks made of 50 slices.</p> <p>The dataset of <em>atomic force microscopy </em>(AFM) is included in one ZIP archive "AFM_YoungModulus_SetpointHeight.zip", which includes data on Young modulus and Setpoint Height of cell lines 22Rv1, PNT1A and PC-3 and treatments zinc, docetaxel, cisplatin (+control), i.e. identical like for confocal microscopy. The file naming is as follows: "AFM_cellline_treatment_FOV_Youngmodulus.tif" for Young modulus and "AFM_cellline_treatment_FOV_setpointheight.tif" for setpoint height. The data are filtered 32-bit tiff images, where the pixel value correspond to cell stiffness (young modulus) in Pa or setpoint height in m.</p> <p><em>Confocal microscopy analysis files</em></p> <p>Following files are csv tables including image analysis of actin/tubulin staining captured by confocal microscope:</p> <p>Cytoskeleton_fluo_analysis_Cell_Cell_periphery_morphology.csv: table includes analyzed data for actin and tubulin staining in following cellular regions: cell, cell periphery. Standard ImageJ parameters regarding intensity and morphology included.</p> <p>Cytoskeleton_fluo_analysis_Fibers.csv: table includes results of manual segmentation and consequent analysis of actin stres fibers in the cells. Apart from standard ImageJ parameters, also number of stress fibers per cell and standard deviation of fiber angle relative to the cell mean angle (for details see methods) are included.</p>
Atomic Force Microscopy Images of Various Specimens
<p>This data set consists of ten atomic force microscopy images in MI format as well as corresponding previews in PNG format.</p> <p>The microscopy images are of various materials and have been scanned with AFM equipment from Keysight Technologies. Details on the individual images:</p> <ul> <li>image_7.mi - calibration grid with 5 µm pitch size</li> <li>image_8.mi - Celgard (a polymer membrane used in batteries)</li> <li>image_9.mi - Titanium-Tungsten film</li> <li>image_10.mi - AFM image</li> <li>image_11.mi - self-assembled monolayer of lipids on gold</li> <li>image_12.mi - capacity calibration sample for Scanning Microwave Microscopy imaging</li> <li>image_13.mi - capacity calibration sample for Scanning Microwave Microscopy imaging</li> <li>image_14.mi - PS-LDPE-12M (a polymer blend of Polystyrene and Polyolefin Elastomere)</li> <li>image_15.mi - AFM Calibration grid</li> <li>image_16.mi - AFM Calibration grid</li> </ul> <p>The images can be opened using, e.g. Gwyddion: http://gwyddion.net/<br /> The Python package Magni can be used to load the images into Python (using the magni.afm.io module): https://github.com/SIP-AAU/Magni</p> <p>The images are provided as-is without warranty of any kind.</p>
Atomic Force Microscopy Images of Cell Specimens
<p>This data set consists of seven atomic force microscopy images in MI format as well as corresponding previews in PNG format.</p> <p>The microscopy images are of cell material and have been scanned with AFM equipment from Keysight Technologies. Details on the individual images:</p> <ul> <li>image_0.mi - Chinese hamster ovary cells</li> <li>image_1.mi - Chinese hamster ovary cells</li> <li>image_2.mi - human bladder carcinoma cells</li> <li>image_3.mi - human bladder carcinoma cells</li> <li>image_4.mi - Chinese hamster ovary cells</li> <li>image_5.mi - Chinese hamster ovary cells</li> <li>image_6.mi - Chinese hamster ovary cells</li> </ul> <p>The images can be opened using, e.g. Gwyddion: http://gwyddion.net/<br /> The Python package Magni can be used to load the images into Python (using the magni.afm.io module): https://github.com/SIP-AAU/Magni</p> <p>The images are provided as-is without warranty of any kind.</p>
Algorithms for Reconstruction of Undersampled Atomic Force Microscopy Images Dataset
<p>This deposition contains the results from a simulation of reconstructions of undersampled atomic force microscopy (AFM) images. The reconstructions were obtained using a variety of interpolation and reconstruction methods.</p> <p>The deposition consists of:</p> <ol> <li>An HDF5 database containing the results from simulations of reconstructions of undersampled atomic force microscopy images (reconstruction_goblet_ID_0_of_1.hdf5).</li> <li>The Python script which was used to create the database (reconstruction_goblet.py).</li> <li>Auxillary Python scripts needed to run the simulations (optim_reconstructions.py, it_reconstruction.py, interp_reconstructions.py, gamp_reconstructions.py, and utils.py).</li> <li>MD5 and SHA256 checksums of the database and Python script files (reconstruction_goblet.MD5SUMS, reconstruction_goblet.SHA256SUMS).</li> </ol> <p>The HDF5 database is licensed under CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/) . Since the CC BY 4.0 license is not well suited for source code, the Python script is licensed under the BSD 2-Clause license (http://opensource.org/licenses/BSD-2-Clause) .</p> <p><strong>The files are provided as-is with no warranty as detailed in the above mentioned licenses.</strong></p> <p>The simulation results in the database are based on "Atomic Force Microscopy Images of Cell Specimens" and "Atomic Force Microscopy Images of Various Specimens" by Christian Rankl licensed under CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). The original images are available at http://dx.doi.org/10.5281/zenodo.17573 and http://dx.doi.org/10.5281/zenodo.60434. The original images are provided as-is without warranty of any kind. Both the original images as well as adapted images are part of the dataset. </p>
Dataset of the publication: Atomic Force Microscopy beyond Topography: Chemical Sensing of 2D Material Surfaces through Adhesion Measurements
<p>Dataset of the publication: Atomic Force Microscopy beyond Topography: Chemical Sensing of 2D Material Surfaces through Adhesion Measurements</p> <p>DOI: 10.1021/acsami.3c19254</p> <p><span><span>I. Brotons-Alcázar, Jason. S. Terreblanche, S. Giménez-Santamarina, G. M. Gutiérrez-Finol, K. S. Ryder, A. Forment-Aliaga, E. Coronado, <em>ACS Appl. Mater. Interfaces</em> <strong>2024</strong>, <em>16</em>, 19711.</span> </span></p>
Data Grids for examples in Probe Particle Atomic Force Microscopy simulation program (ppafm)
<p>These files are used for running the examples for [ppafm](https://github.com/Probe-Particle/ppafm/) program.</p> <p>The grids are stored in in [.xsf](http://www.xcrysden.org/doc/XSF.html) and [.cube](https://paulbourke.net/dataformats/cube/) format.</p> <p>The data set compiles both the new examples used in paper [Advancing scanning probe microscopy simulations: A decade of development in probe-particle models](https://www.sciencedirect.com/science/article/pii/S0010465524002649) as well as older examples.</p> <p>Notice that the structure does not exactly reflect the directory structure in the [example folder of ppafm](https://github.com/Probe-Particle/ppafm/tree/main/examples) to prevent possible redudancy, but is instead flatenized and sorted by molecules.</p>
Atomic Force Microscopy image of coagulation factor Va in liquid
<p>Original raw and corrected AFM images of isolated coagulation factor Va (FVa). The image was acquired in liquid with an OTR8 cantilever using the peak force tapping mode of a multimode V microscope. The image size is 1 x 1 µm² with 1024 x 1024 pixels². The corrected image was obtained using Gwyddion (.gwy file) from the raw image file (.spm). This image was the experimental data used to assemble the A trimer and the two C domains of FVa using the AFMAssembly pipeline described in Chaves et al. (2014): http://dx.doi.org/10.1160/TH14-06-0481. The paper can be downloaded from the HAL repository (https://hal.archives-ouvertes.fr/hal-01146300v1).</p>
METADATA for results of irradiation-induced complex DNA damage measurements using plasmid pBR322 along a typical Proton Treatment Plan at the MedAustron proton and carbon beam therapy facility (energy 137–198 MeV and Linear Energy Transfer (LET) range 1–9 keV/μm), by means of Agarose Gel Electrophoresis and DNA fragmentation using Atomic Force Microscopy (AFM)
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Figure 2 in High-Resolution Functional Imaging of Native Proteins using Force Distance Curve Based Atomic Force Microscopy
Figure 2. - Juvenile Trachipterus arcticus, 129 mm SL, collected at Faial Island, Azores, 14 May 2014, on the surface. A: Portrait with anterior black facet visible; B: Oblique lateral view with first spines erected; note orange bulbous outgrowths on the prolonged spine; C: Lateral view showing proportions, markings and orientation of fins. Scale bars: A = 1 cm; B, C = 5 cm.
Figure 1 in High-Resolution Functional Imaging of Native Proteins using Force Distance Curve Based Atomic Force Microscopy
Figure 1. - Adult Trachipterus arcticus, about 1.8 m long, observed south of Pico Island, Azores, 18 Aug. 2013, 950 m deep.
Raman spectroscopic mapping and atomic force microscopy statistical analyses for the determination of WS2 flake thickness
<p><span>This database contains the statistical analyses carried out in order to evaluate the thickness of the WS</span><sub><span>2</span></sub><span> nanoflakes. In order to have a reliable comparison we determine the methodology of comparing Raman spectroscopic mapping and atomic force microscopy (AFM). </span></p> <p><span>In case of Raman spectroscopy, the thickness is evaluated by employing the separation of the two vibrational mode, namely E</span><sub><span>2g</span></sub><span> and A</span><sub><span>1g</span></sub><span>. This method is well-established and the number of layers has been previously tabulated in different articles. </span></p> <p><span>Each spectrum of the Raman analysis, is performed with a 100X objective in a confocal microscope, with a 473 nm laser excitation, a laser power of 0.5 mW and an acquisition time of 1 s.</span></p> <p><span>The AFM analysis are carried out in tapping mode with a 512-pixel x 512-pixel resolution and and a scan rate of 1Hz per line.</span></p>
Data for publication: Nanomechanical and Structural Study of Au38 Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity
<p>Original data of Figures published in:</p> <p><strong>Nanomechanical and Structural Study of Au<sub>38</sub> Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity</strong></p> <p>Journal of Colloid and Interface Science, 2022, Michal Swierczewski<sup>,</sup> Alexis Chenneviere, Lay-Theng Lee, Plinio Maroni and Thomas Bürgi*<sup>[</sup></p> <p> </p>
Data from "Quantitative determination of atomic buckling of silicene by atomic force microscopy"
<p>Data From the publication "Quantitative determination of atomic buckling of silicene by atomic force microscopy"</p>
dataset for "Atomic force microscopy characterization of Polyester Grafted with poly(styrene sulfonate)"
<p>Atomic Force Microscopy (AFM) raw files of polycaprolactone (PCL) and polyethylene terephthalate (PET) non-functionalized and functionalized with poly(sodium 4-styrene sulfonate) (PNaSS) by thermal radical grafting, thermal radical grafting in the presence of redox initiator (Mohr's salt), and UV grafting. </p> <p>https://chemrxiv.org/engage/chemrxiv/article-details/60c75963842e650a5edb49f6</p> <p>DOI: 10.26434/chemrxiv.14687556</p>
Atomic force microscopy of transfer film development
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AFM data of ice clusters on Cu(111) and Au(111) in paper "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Frequency shift CO-tip atomic force microscopy data of small ice clusters on Cu(111) and Au(111) surfaces as they appear in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains each experiment as a Numpy .npz file. Each file contains the measurement data as a 3D array in the key 'data' and the physical extent of the scan region in the x and y directions in Ånströms in the keys 'lengthX' and 'lengthY'.</p>
Hartree potentials and geometries of relaxed on-surface ice clusters in "Structure discovery in Atomic Force Microscopy imaging of ice"
<p>Hartree potentials and geometries of on-surface DFT-relaxed ice clusters used in the paper "Structure discovery in Atomic Force Microscopy imaging of ice".</p><p>The data are saved in a compressed .tar.gz archive. The unpacked archive contains the data for each ice cluster in the .xsf format. The density functional theory (DFT) calculations were done using the Vienna Ab-initio Simulation Package with the optB86b-vdW density functional.</p>
High-Speed Atomic Force Microscopy Highlights New Molecular Mechanism of Daptomycin Action
<p>Data underlying the figures in the publication “High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action”, published in <em>Nat Commun, </em><strong>2020</strong>, 11, 6312. <a href="https://doi.org/10.1038/s41467-020-19710-z">https://doi.org/10.1038/s41467-020-19710-z</a></p> <p>Table of contents:</p> <p><strong>1.</strong> <strong>Movie 1</strong>; HS-AFM movie of the first minutes after exposure to sub-MIC Dap on a POPG supported membrane. Guides to the eye highlights those oligomers identifiable. Movie parameters: frame rate 33 ms; full image of 90 nm x 65 nm and 256x180 pixels; colour depth 8bit (256 values); full colour scale 4 nm.</p> <p><strong>2. </strong><strong>Movie 2</strong>; HS-AFM movie after tens of minutes after exposure to sub-MIC Dap that shows diffusing dimples on a POPG supported membrane which interact by swinging trajectories. Movie parameters: frame rate 83 ms; full image of 150nm x 150nm and 256x256 pixels; colour depth 8bit (256 values); full colour scale 4 nm.</p> <p><strong>3. </strong><strong>Movie 3</strong>; HS-AFM movie of the first minutes after exposure to over-MIC of a POPG supported membrane. A flow of material is visualized thanks to the motion of the ripples, it starts at the lm3m cubic phase (left) and ends at a tubulation (right). Movie parameters: frame rate 456 ms; full image of 400nm x 400nm and 300x300 pixels; colour depth 8bit (256 values); full colour scale 16 nm.</p> <p><strong>4. </strong><strong>Movie 4</strong>; HS-AFM movie of the cyclic accumulation of material in the pores created on TOCL/POPG supported membranes under the exposure of the outer leaflet to supplementary quantities of Dap added to the imaging solution. The process seems to eject material out of the membrane; see the material that appears next to the pore at 1.30s. Movie parameters: frame rate 260 ms; zoom of a full image of 140nm x 100nm and 256x180 pixels; colour 29 depth 8bit (256 values); full colour scale 3 nm.</p>
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