The R Journal: accepted article

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afmToolkit: an R Package for Automated AFM Force-Distance Curves Analysis PDF download
Rafael Benítez, Vicente J. Bolós and José-Luis Toca-Herrera

Abstract Atomic force microscopy (AFM) is widely used to measure molecular and colloidal inter actions as well as mechanical properties of biomaterials. In this paper the afmToolkit R package is introduced. This package allows the user to automatically batch process AFM force-distance and force-time curves. afmToolkit capabilities range from importing ASCII files and preprocessing the curves (contact point detection, baseline correction. . . ) for finding relevant physical information, such as Young’s modulus, adhesion energies and exponential decay for force relaxation and creep experiments. This package also contains plotting, summary and feature extraction functions. The package also comes with several data sets so the user can test the aforementioned features with ease. The package afmToolkit eases the basic processing of large amount of AFM F-d/t curves at once. It is also flexible enough to easily incorporate new functions as they are needed and can be seen as a programming infrastructure for further algorithm development.

Received: 2017-04-07; online 2017-10-12
CRAN packages: afmToolkit, devtools, ggplot2, minpack.lm, gridExtra, scales, dplyr , CRAN Task Views implied by cited CRAN packages: ChemPhys, Graphics, Optimization, Phylogenetics

CC BY 4.0
This article is licensed under a Creative Commons Attribution 4.0 International license.

  author = {Rafael Benítez and Vicente J. Bolós and José-Luis Toca-
  title = {{afmToolkit: an R Package for Automated AFM Force-Distance
          Curves Analysis}},
  year = {2017},
  journal = {{The R Journal}},
  url = {}