Mica was freshly cleaved with tape prior to being functionalized with an aqueous solution of poly-Llysine (0.01 %) by drop-casting (40 µL) of the solution. After 30 s, the poly-L-lysine was washed off with ultra-pure water and dried under a nitrogen flow. Aqueous CNCs suspensions (0.0001 wt%, 40 µL) were then drop cast onto the functionalized mica surface. The samples were left to dry either at room temperature (T1) or at 75 °C (T2). The images were acquired with a Park NX10 microscope, in tapping mode with TAP300Al-G probes at room temperature. Images were recorded with 4096 × 4096 pixels of resolution in a 25 μm × 25 μm, and were subsequently cropped in Illustrator to have a final image of 5 μm × 5 μm. The CNC length and height (representing the cross-section) were measured using the XEI software (Park Systems) on more than 1000 rods. The aspect ratio of the CNCs was calculated by dividing the length of the CNCs by their height, and aspect ratio's lower than 10 were removed manually as these are impurities which do not fit the definition of CNCs. 45 The reported confidence intervals are the standard deviation of the average particle dimensions.
Xei software
Manufactured by Park Systems
Sourced in Denmark, United States
The XEI software is a data acquisition and analysis software developed by Park Systems. It is designed to work seamlessly with Park Systems' atomic force microscopes (AFMs) and provides a user-friendly interface for controlling the instrument, acquiring data, and analyzing the results.
Automatically generated - may contain errors
Lab products found in correlation
Ppp nchr, by Park Systems (3 mentions)
Milli q water, by Merck Group (3 mentions)
Xe 100 afm system, by Park Systems (3 mentions)
Noran system 7, by Thermo Fisher Scientific (3 mentions)
Xe 100, by Park Systems (3 mentions)
Nx 20 instrument, by Park Systems (3 mentions)
Contscr cantilevers, by NanoWorld (2 mentions)
Xe 100 atomic force microscope, by Park Systems (2 mentions)
Pyrrole, by Merck Group (2 mentions)
Xe 100 instrument, by Park Systems (1 mentions)
Phosphate buffered saline (pbs), by Avantor (1 mentions)
Park nx20, by Park Systems (1 mentions)
Xe 70, by Park Systems (1 mentions)
Xe 100 microscope, by Park Systems (1 mentions)
Axis supra, by Shimadzu (1 mentions)
Easydrop, by Krüss (1 mentions)
3 aminopropyltriethoxysilane, by Merck Group (1 mentions)
V1 afm mica discs, by Ted Pella (1 mentions)
Xe 100 afm, by Park Systems (1 mentions)
Xep software, by Park Systems (1 mentions)
44 protocols using xei software
1
Mica Functionalization and CNC Deposition
2
Characterization of Polymer-Coated Electrodes
3
Nanoparticle Characterization by AFM
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Freshly cleaved mica sheets (Agar Scientific) were cut to produce 7×7 mm substrates. 50 µL of the concentrated raw water sample was deposited onto the mica sheets. The samples were covered for one hr and then residual liquid was wicked away with a tissue. The mica substrates were washed 4 times by immersion in 25 mL aliquots of ultrapure water for 30 s, to remove any residual salts, and air-dried overnight at room temperature under a dessicator lid to stop air-borne particles falling on the samples.
Sizes and shapes of the nanoparticles were obtained by AFM using a XE100 instrument (Park Systems). The samples were analysed in non-contact mode using a Si cantilever (PPP-NCHR, Park Systems). Images covering and area of 10 x10 µm were acquired, and heights of particles were measured using the XEI software (Park Systems).
Sizes and shapes of the nanoparticles were obtained by AFM using a XE100 instrument (Park Systems). The samples were analysed in non-contact mode using a Si cantilever (PPP-NCHR, Park Systems). Images covering and area of 10 x10 µm were acquired, and heights of particles were measured using the XEI software (Park Systems).
4
Topographic Imaging of Trypanosoma cruzi Extracellular Vesicles
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Topographic imaging of the EV of T. cruzi was performed using the non-contact AFM mode in an NX-20 instrument (Park Systems, Suwon, Korea) with ACTA cantilevers (K = 40 N m–1 and f = 320 kHz), as previously described13 (link). Briefly, each EV sample was diluted 1:4 in sterile-filtered PBS and 8 µL of the dilution of EV was deposited onto freshly cleaved muscovite mica. After 10 min, the substrate with the sample was rinsed three times with MilliQ water (Millipore, Burlington, MA, USA) and further dried with a gentle stream of argon. Images were typically acquired as 256 × 256 pixels at a scan rate of 0.5–0.7 Hz, and processed and analyzed using XEI software (Park Systems, Suwon, Korea). Representative images of samples were obtained by scanning at least 3 different locations on at least 3 different samples.
5
AFM Characterization of Protein Fibrils
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AFM was performed on freshly cleaved mica discs that are positively functionalized with 1% (3-aminopropyl)triethoxysilane (APTS) in an aqueous solution for 3 min at RT. For the fibril deposition onto the substrates, 20-μl aliquots each containing a 50 μM protein solution was loaded on the surface of mica discs at predefined time points. Deposition lasted 3 min and was followed by a gentle drying by nitrogen flow. The mica discs were stored in a desiccator for 1 day before imaging to avoid prolonged exposure to atmospheric moisture. AFM imaging was performed at RT by a Park NX10 operating in true noncontact mode that was equipped with a super sharp tip (SSS-NCHR) Park System cantilever. The length and height quantifications were performed manually using XEI software developed by Park Systems Corporation.
6
Atomic Force Microscopy of Doxorubicin-Treated Cells
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Cells (1 × 104 per 6-cm dish) were plated (SPL Life Sciences), pretreated with PJ-34 for 1 h, and subsequently co-treated with DOX for 72 h. Supernatants were removed, and cells were fixed with 3.7% formaldehyde for 15 min. Fixed cells were washed with PBS (AMRESCO) and deionized water and were then dried. All AFM images were acquired on an XE-100 AFM system (Park Systems Corp., Suwon, Korea) in noncontact AFM mode with a CNT/AFM cantilever, which had a resonance frequency of 310 kHz. AFM image analysis was carried out using XEI software (Park Systems, Inc.).
7
PDMS Surface Characterization with Molecular Coatings
8
Orthodontic Bracket Surface Roughness Analysis
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Two types of orthodontic brackets were investigated, conventional metal brackets (ORMCO mini diamond bracket) and self-ligating metal brackets (Damon Q) were used. Sixteen conventional metal brackets Group 1 and Self-ligating metal brackets Group 2 were used in this study. To analyze the surface roughness all the untreated brackets were coded and analyzed using AFM then the coded brackets were grouped accordingly. 15 ml of deionized water was used as a control group, and the mouthwashes used were 15 ml of herbal mouthwash (HIORA), 15 ml of chlorhexidine mouthwash (Chlorex ADS), and 15 ml of betadine mouthwash. All the brackets were evenly grouped and individually immersed for a period of seven days at room temperature and after exposure, they were subjected to surface characteristics changes using AFM.
The images were scanned with 30 mm × 30 μm in size and a total of 32 images were collected. The data acquisition and image processing were performed with XEI Software from Park Systems for roughness analysis [Figure 1 ], and a plane correction was performed on all images and quantitatively analyzed.
The parameters analyzed were roughness average (Ra) root mean square roughness (Rq) and peak to valley height of roughness profile (Rpv) were tabulated and analyzed.
The images were scanned with 30 mm × 30 μm in size and a total of 32 images were collected. The data acquisition and image processing were performed with XEI Software from Park Systems for roughness analysis [
The parameters analyzed were roughness average (Ra) root mean square roughness (Rq) and peak to valley height of roughness profile (Rpv) were tabulated and analyzed.
9
Bacterial Surface Characterization by AFM
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AFM measurements were performed in air with an XE-70 (Park Systems) at room temperature in noncontact mode with an ACTA silicon cantilever (Applied Nanostructures) with a nominal resonance frequency of 300 kHz and a nominal force constant of 37 N/m. Samples were grown as previously described and air dried for imaging. Measurements began by scanning a random area of 30 by 30 μm, which was gradually decreased until the bacterial surface could be observed in detail. Topography, amplitude, and phase images measuring 7.5 by 7.5 μm were recorded simultaneously. The acquired data were converted into topography, amplitude, and phase images and analyzed with XEI software (Park Systems). AFM imaging also allowed cell surface roughness measurement. A roughness average (Ra), meaning the average distance from the roughness profile to the center plane of the profile, was obtained from the acquired topography images.
10
Plasma-Induced Surface Modifications Analyzed by AFM and SEM
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The modifications encountered upon exposure of the substrates to various plasma configurations and experimental conditions were evaluated by means of AFM and, respectively, SEM techniques for characterization of surface topography and morphology. AFM images were recorded with a Park Systems XE-100 microscope (Suwon, Korea) operating in non-contact mode, for various areas; herein we presented data recorded over areas of 5 × 5 μm2. The analysis of the AFM data was carried out using the “XEI” software from Park Systems (version 1.7.6). First order line by line flattening was applied. Points with larger height (corresponding to the grains) were excluded from this line fitting using a height threshold mask. RMS values were calculated for one image, for each sample. SEM measurements were performed on a FEI S Inspect high-resolution microscope (Hillsboro, OR, USA), operating at an accelerating voltage of 5 kV. In order to prevent charge accumulation on the surface, the samples were coated with a very thin gold layer (5 nm) deposited by the magnetron sputtering technique.
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