Nanoscope analysis software version 1

Manufactured by Bruker

Sourced in United States

The NanoScope Analysis Software version 1.5 is a comprehensive data analysis software designed for Bruker's atomic force microscopes (AFMs). The software provides a powerful suite of tools for processing, analyzing, and visualizing AFM data. It supports a wide range of data formats and enables users to extract quantitative information from their AFM measurements.

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Lab products found in correlation

Dimension fastscan afm, by Bruker (2 mentions) Dnp 10 d tip, by Bruker (2 mentions) Nanoscope 5, by Bruker (2 mentions) Scanasyst air, by Bruker (2 mentions) Nanoscope 5 controller, by Bruker (2 mentions) Fastscan a probes, by Bruker (1 mentions) F7013, by Agar Scientific (1 mentions) Dimension icon microscope, by Bruker (1 mentions) Dimension icon afm, by Bruker (1 mentions) Ppp nch, by Nanosensors (1 mentions) Bioscope catalyst atomic force microscope, by Bruker (1 mentions) G250 2 mica sheets, by Agar Scientific (1 mentions) Peakforce qnm scanning probe microscope, by Digital Instruments (1 mentions)

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NanoScope Analysis software (148 citations) NanoScope Analysis 1.5 (106 citations) NanoScope Analysis (63 citations) NanoScope software (50 citations) NanoScope Analysis version 1.5 (6 citations) Nanoscope analysis software 1.8 (3 citations)

10 protocols using nanoscope analysis software version 1

Atomic Force Microscopy of Rad50 Interactions

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All dry and fluid samples were imaged using the Dimension FastScan Bio Atomic Force Microscope (Bruker) in tapping mode.
For dry imaging, FastScan A probes (Bruker) with a spring constant of 18 N/m were tuned to a resonance frequency between 800 and 2,000 kHz and the amplitude setpoint was adjusted to the highest possible setting, so as to ensure little noise and minimizes the force the sample is exposed to. In fluid, FastScan D probes were used, with a spring constant of 0.25 N/m (resonance frequency of 90 to 140 kHz).
Fast-scan images were captured with a scan area of 1 to 2 µm, a scan rate of 15.1 Hz, and with 512 samples per line. For conventional AFM, images were captured at 1.8 frames per minute at room temperature.
Rad50 coiled-coil interactions with the DNA substrate during fast-scan imaging in fluid, as presented in Fig. 4A, were identified manually using similar interactions observed from AFM imaging in air data (Fig. 3) as a reference; see SI Appendix for further details.
All AFM images presented, excluding Fig. 6C, were processed using the Nanoscope Analysis software version 1.5 by Bruker Corporation. Fig. 6C was processed using SPIP software. Movies were produced using Windows Movie Maker.

Zabolotnaya E., Mela I., Williamson M.J., Bray S.M., Yau S.K., Papatziamou D., Edwardson J.M., Robinson N.P, & Henderson R.M. (2020). Modes of action of the archaeal Mre11/Rad50 DNA-repair complex revealed by fast-scan atomic force microscopy. Proceedings of the National Academy of Sciences of the United States of America, 117(26), 14936-14947.

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Probing Zebrafish Embryo Biomechanics

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Live zebrafish embryos (48 hpf) were anesthetized using 1x tricaine in egg water and mounted on PDMS gels. The tips of fish tails were probed using a DNP-10 D tip (Bruker, nominal stiffness ~0.06 N/m) on a Bruker Dimension FastScan AFM immersed in egg water containing 1x tricaine. Probe deflection sensitivity was calibrated by taking indentation curves on glass and the nominal tip stiffness was calibrated by thermal tuning (assuming a simple harmonic oscillator in water). Force vs. deflection curves were collected for a ramp size of 1.5μm at a rate of 750 nm/s for at least 2 locations per fish, with 10–11 fish measured per group. The first 600nm of the extension curves were fit with NanoScope Analysis Software version 1.5 (Bruker) assuming a Poisson’s ratio of 0.5 and using the Sneddon fit model⁷¹.

Moro A., Discroll T., Boraas L.C., Armero W., Kasper D.M., Baeyens N., Jouy C., Mallikarjun V., Swift J., Ahn S.J., Lee D., Zhang J., Gu M., Gerstein M., Schwartz M, & Nicoli S. (2019). microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis. Nature cell biology, 21(3), 348-358.

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Probing Zebrafish Embryo Biomechanics

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Peptide Fibrils Characterization via AFM

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The peptide samples were diluted to 0.05 mg/ml in a solution of HCl (pH2, using filter sterilised milli-Q water). 20 μl of sample was deposited onto freshly cleaved mica (Agar scientific, F7013) and incubated for 10 minutes. Following incubation, the sample was washed with 1 ml of filter sterilised milli-Q water and then dried using a stream of nitrogen gas. Fibrils were imaged using a Multimode AFM with a Nanoscope V (Bruker) controller operating under peak force tapping mode with ScanAsyst probes (silicon nitride triangular tip with tip height = 2.5-2.8 μm, nominal tip radius = 2 nm, nominal spring constant 0.4 N/m, Bruker). Images were collected with a scan size of 6 x 6 μm with 2048 x 2048 pixel resolution. A scan rate of 0.305 Hz was used with a noise threshold of 0.5 nm and the Z limit was reduced to 1.5 μm. The peak force set point was set automatically, typically to ~675 pN during image acquisition. Nanoscope analysis software (Version 1.5, Bruker) were used to process the image data by flattening the height topology data to remove tilt and scanner bow.

Lutter L., Serpell C.J., Tuite M.F., Serpell L.C, & Xue W.F. (2020). Three-dimensional reconstruction of individual helical nano-filament structures from atomic force microscopy topographs. Biomolecular concepts, 11(1).

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Atomic Force Microscopy of HNTs and Cells

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Atomic force microscopy (AFM) images of HNTs and cells were made using a Dimension Icon microscope (Bruker) operating in PeakForce Tapping mode. ScanAsyst-air (Bruker) probes were used to obtain images (nominal length 115 μm, tip with a radius of 2 nm, spring stiffness 0.4 N m^–1). Images were obtained at 512–1024 scan lines at a scanning speed of 0.8–0.9 Hz. The adhesion of the nanoparticles was analyzed using an atomic force microscope and calculated from 30 × 30 nm sites on the nanoparticles surface. The obtained data were processed using Nanoscope Analysis software version 1.7 (Bruker).

Guryanov I., Naumenko E., Akhatova F., Lazzara G., Cavallaro G., Nigamatzyanova L, & Fakhrullin R. (2020). Selective Cytotoxic Activity of Prodigiosin@halloysite Nanoformulation. Frontiers in Bioengineering and Biotechnology, 8, 424.

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AFM Analysis of CNC and FITC-CNC Morphology

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AFM was conducted to study the morphology and dimension (length and diameter) of CNC and FITC-CNC. Diluted never-dried CNC and FITC-CNC were dropped onto a glass slide and allowed to air dry. Samples were scanned at room temperature, in tapping mode with OMCL-AC160TS standard Si probes (tip radius < 10 nm, spring constant = 2.98 N/m, resonant frequency = ~310kHz) using the Dimension Edge with High-Performance AFM (Bruker, Sant Barbara, CA, USA) equipment. AFM micrographs were analyzed using Bruker Nanoscope analysis software (Version 1.7) operated using Peak/Force tapping mode with one controller (Nanoscope V from Bruker) for evaluating the length and width of the samples.

Shazali N.A., Zaidi N.E., Ariffin H., Abdullah L.C., Ghaemi F., Abdullah J.M., Takashima I, & Nik Abd. Rahman N.M. (2019). Characterization and Cellular Internalization of Spherical Cellulose Nanocrystals (CNC) into Normal and Cancerous Fibroblasts. Materials, 12(19), 3251.

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Characterization of Nanostructured Gold Surfaces

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The Atomic Force Microscopy Multimode Nanoscope IV from Bruker (Palaiseau, France) was used to characterize the nanostructured gold surfaces (plain gold layer and nanoantennas substrates, both, with and without lipid bilayers). The plain gold layer and Au nanoantennas substrates were prepared using the immobilization procedure described above. The lipid immobilization on the substrates was observed before chloroform rinsing for control purposes (data not shown) and after chloroform rinsing.
To probe the samples topography, a Peak Force Tapping mode (ScanAsyst) in dry state was selected using silicon nitride tips (SCANASYST-AIR from Bruker, having a spring constant “k” of around 0.4 Nm⁻¹). The images were obtained preferably along the fast scan axis at a scan rate of 1 Hz with a resolution of 512 × 512 pixels. The data analysis was performed using NanoScope Analysis Software (version 1.7) from Bruker (Palaiseau, France).

Omeis F., Boubegtiten-Fezoua Z., Seica A.F., Bernard R., Iqbal M.H., Javahiraly N., Vergauwe R.M., Majjad H., Boulmedais F., Moss D, & Hellwig P. (2021). Plasmonic Resonant Nanoantennas Induce Changes in the Shape and the Intensity of Infrared Spectra of Phospholipids. Molecules, 27(1), 62.

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Atomic Force Microscopy Characterization of Ni3B Nanoparticles and Phages

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Ni₃B nanoparticles, phages and compounds of phages with Ni₃B were characterised with an atomic force microscope (AFM). The measurements were carried out on a Dimension Icon AFM with a Nanoscope V controller (Bruker, Santa Barbara, California) in ambient conditions. The measurements were performed in tapping mode, to minimise the lateral interaction. Silicon cantilevers (PPP NCH, Nanosensors) with a nominal resonance frequency of 330 kHz, spring constant of 42 Nm^-1, and a nominal tip diameter of less than 10 nm were used. All images were taken at a resolution of 512 × 512 pixel². M13 phages were incubated with 10 mg of amorphous and crystalline Ni₃B nanoparticles at a concentration of 3 × 10¹² pfu/ml in 1 ml TBS supplemented with 0.8% Tween-20. After 2 h, unbound phages were removed by washing the substrates three-times with TBS. Samples were prepared by dropping the sample suspension on a silicon wafer or freshly cleaved mica. The samples were dried in a stream of dry nitrogen. Image analysis and processing was performed with the Nanoscope Analysis software Version 1.40 (Bruker). A plane correction procedure and a line by line fit were used to compensate for the sample tilt.

Ploss M., Facey S.J., Bruhn C., Zemel L., Hofmann K., Stark R.W., Albert B, & Hauer B. (2014). Selection of peptides binding to metallic borides by screening M13 phage display libraries. BMC Biotechnology, 14, 12.

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Atomic Force Microscopy of HePS and Bacteria

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A lyophilized HePS was dissolved in Milli-Q water to obtain a 1 mg/L solution. A 2-μL aliquot of the HePS solution was deposited onto a freshly cleaved mica surface and left to
dry for 30 min at an ambient temperature of around 22°C. To observe the bacterial cells and HePS in the culture medium simultaneously, 2 µL of the culture medium was collected
during cultivation, diluted 100 times using ion exchanged water, deposited onto a freshly cleaved mica sheet, and left to dry for 2 hr in a desiccator. Topographical imaging was
performed in air using a BioScope Catalyst atomic force microscope (Bruker, Santa Barbara, CA, USA) operated in peak force tapping mode using a NanoScope V controller (Bruker).
Obtained images were flattened using NanoScope Analysis software version 1.40 (Bruker).

MENGI B., IKEDA S., MURAYAMA D., BOCHIMOTO H., MATSUMOTO S., KITAZAWA H., URASHIMA T, & FUKUDA K. (2020). Factors affecting decreasing viscosity of the culture medium during the stationary growth phase of exopolysaccharide-producing Lactobacillus fermentum MTCC 25067. Bioscience of Microbiota, Food and Health, 39(3), 160-168.

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Characterizing Lipid Nanoparticle Surface Morphology

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For AFM experiments, 3 µL of RTA loaded and unloaded SLN were deposited onto a freshly cleaved mica surface ((G250-2 mica sheets 1" x 1" x 0.006"; Agar Scientific Ltd, Essex, UK), and left to dry for 1 h before AFM imaging. The images were obtained by scanning the mica surface, in air, under ambient conditions using a PeakForce QNM Scanning Probe Microscope (Digital Instruments, Santa Barbara, CA, USA; Bruker Nanoscope analysis software Version 1.40). The AFM measurements were obtained using ScanAsyst-air probes, and the spring constant (0.67 N/m; nominal 0.4 N/m) and deflection sensitivity were calibrated, but not the tip radius (a nominal value of 2 nm was used). Surface roughness (Ra) values were determined by entering surface scanning data into a digital levelling algorithm (Bruker Image Analysis Nanoscope Analysis software V 1.40). AFM images were collected from two different samples by random spot surface sampling (at least five areas).

Akanda M.H., Rai R., Slipper I.J., Chowdhry B.Z., Lamprou D., Getti G, & Douroumis D. (2015). Delivery of retinoic acid to LNCap human prostate cancer cells using solid lipid nanoparticles. International journal of pharmaceutics, 493(1-2).

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