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Spm data processing

Manufactured by Bruker

SPM Data Processing is a software package that enables the analysis and processing of data acquired from scanning probe microscopy (SPM) techniques. The core function of this software is to provide users with tools for visualizing, analyzing, and interpreting SPM data, without making any interpretations or extrapolations about its intended use.

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3 protocols using spm data processing

1

Quantifying Tissue Elasticity via AFM

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The AFM images and FD curves were analyzed using JPK SPM data Processing Version 6.1.172. A Hertzian model, with a spherical tip shape and a Poisson ratio of 0.5, was fit to the approach part of the force–indentation curves to quantify the apparent Young’s modulus (E apparent). To remove the effects of proteins and debris floating on the tissue surface, the curves were fit after the contact point, from 1 to 5nN. After confirming the Gaussian distribution for each biological sample (n = 7 at E12.5, n = 7 at E14.5, and n = 3 at P1), the values of Young’s modulus were pooled together for each stage. Outliers of the Young’s modulus values at each stage were detected using the ROUT method (Q = 0.1%) and removed.
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2

Atomic Force Microscopy of Thylakoid Membranes

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Two microliters of thylakoid membrane samples were adsorbed onto freshly cleaved mica surface with 38 μL of adsorption buffer (10 mM Tris-HCl, pH 7.5, 150 mM KCl, 25 mM MgCl 2 ) at room temperature for 1.5 h. After adsorption, the sample was carefully rinsed with 800 μL imaging buffer (10 mM Tris-HCl, pH 7.5, 150 mM KCl) 71 (link) . High-resolution imaging was performed in AC imaging mode in liquid at room temperature using a NanoWizard 3 AFM (JPK) equipped with an ULTRA S scanner and Ultra-Short Cantilever probe (0.3 N•m -1 , Nano World) at scan frequencies of 5 Hz using optimised feedback parameters and a resolution of 512 × 512 pixels. The tip spring constant was routinely calibrated. Images were processed with JPK SPM Data Processing (JPK) and ImageJ.
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3

Colloidal Probe AFM of Multilayer Films

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AFM (NanoWizard 3 AFM, JPK Instruments AG, Berlin, Germany) colloidal probe measurements were performed to investigate the surface forces between the multilayer films. The accurate spring constant of the unloaded cantilevers (CSC37/Cr-Au, Mikromasch) was determined by the Sader method. 47 (link) The sensitivity of the cantilevers (loaded, before coating) was obtained by performing force measurements against a bare silica wafer (Supporting Information, Figure S1). A similar procedure as that of the ellipsometry experiment was used herein (40 min stabilization time). A constant approach and retraction speed of 400 nm s -1 was used to avoid hydrodynamic effects. 48 (link) For each condition, three randomly chosen areas (10 μm × 10 μm, 36 points on each area) of the sample were chosen to perform the force measurements. The standard software of the instrument (JPK SPM Data Processing) was utilized to analyze the force curves.
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