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Authors: Ficarra, Elisa; Yoon, S; Benini, L; Macii, E; De Micheli, G.
Authors: Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G.
Published in: IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE
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 approach minimizes processing time with respect to manual and semi-automated DNA sizing. 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%.
Authors: Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G.
Authors: Ficarra, Elisa
Published in: PROCEEDINGS IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING
An automated algorithm is presented to determine fragment DNA size from Atomic Force Microscope images. Several real and synthetic images were tested for different image and fragment sizes and different background noises. The automated approach allows to minimize processing time with respect to manual DNA sizing and to extract information that can be used to perform further analysis on the molecules. For computer-generated test images the percentage error in length estimation is less than 1% and its average value is 0.4%. For real images the deviation with respect to manually-performed length estimation is around 1%.