In thomasgredig/nanoscopeAFM: Load and Analyze Atomic Force Microscopy Data Files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(nanoscopeAFM)
library(ggplot2)
library(scales)
filename = AFM.getSampleImages(type='tiff')
afmd = AFM.import(filename)
plot(afmd)

In order to get more contrast, we can trim 1 percent of the data points as the image may not be in the middle, see the histogram.

AFM.histogram(afmd)

Using the trimPeaks option in plot(), we can remove half from the top and bottom of the histogram and bunch those data points up, so that the contrast enhances.

plot(afmd, trimPeaks = 0.01)

Raster Graph

Graphing a subset of the data points using the AFM.raster() function to obtain the 3D data point set.

dr = AFM.raster(afmd)
head(dr)
# data points higher than 90% of peak
lowerBound = -0.3
upperBound = 0.8
dr1 =dr[which(dr$z>lowerBound & dr$z<upperBound),]
plot(afmd, trimPeaks = 0.01) + 
  geom_raster(data=dr1,fill='white')