Automated DNA fragments recognition and sizing through AFM image processing

This paper presents an automated algorithm to determine
DNA fragment size from atomic force microscope images
and to extract the molecular profiles. The sizing of DNA fragments
is a widely used procedure for investigating the physical properties
of individual or protein-bound DNA molecules. Several atomic
force microscope (AFM) real and computer-generated images were
tested for different pixel and fragment sizes and for different background
noises.The automated approachminimizes processing time
with respect to manual and semi-automatedDNAsizing. Moreover,
the DNA molecule profile recognition can be used to perform further
structural analysis. For computer-generated images, the root
mean square error incurred by the automated algorithm in the
length estimation is 0.6% for a 7.8 nm image pixel size and 0.34%
for a 3.9 nm image pixel size. For AFM real images we obtain a
distribution of lengths with a standard deviation of 2.3% of mean
and a measured average length very close to the real one, with an
error around 0.33%.