Automatic Analysis of Dot Blot Images

Abstract

This paper presents a method for the automatic analysis of macroarray (dot blot) images. The system developed receives as input a dot blot image, corrects it for grid rotation, identifies the visible markers and provides an evaluation of the status of each marker (ON/OFF). Two experiments were carried out to evaluate the detection and classification stages. A total of 222 test images were produced from 6 original dot blot images, with various rotations, translations, contrast and noise level. Over 7500 markers were identified automatically and compared to manual reference. The RMS error in positioning the molecular marker center was between 1.1 and 3.8 pixels and the marker radius error less than 4%. The automatic classification of markers (ON/OFF) was compared to the classification by 3 human experts, using 10 test images. The overall accuracy evaluated on 5118 markers was 94.0%. For those markers that had the same evaluation by all 3 experts, the classification accuracies were 96.6% (ON) and 95.9% (OFF).

Keywords::

• Image processing
• Computer vision
• Macroarray
• Molecular markers

Additional information

Notes on contributors

C.M.R. Caridade

Cristina M.R. Caridade, Assistant professor in Mathematics Department at Coimbra Institute of Engineering, Coimbra, Portugal. She received BSc degree in Mathematics from University of Coimbra (1993) MSC (1999) and PhD (2012) in Applied Mathematics from University of Porto. Her current research interests include the development of algorithms for specific applications in Digital image Processing.

A.R.S. Marcal

André R.S. Marcal received BSc degree in Physics (Solid State Physics) from the University of Porto, Portugal (1991), MSc (1994) and PhD (1998) degrees in Remote Sensing and Image Processing from the University of Dundee, Scotland, UK. He is currently assistant professor in the Mathematics Department, University of Porto.

P. Albuquerque

Pedro Albuquerque received PhD in 2012 from the University of Porto. Currently, he is working as a post-doc researcher at CIBIO (Project: Genomics Applied to Genetic Resources, ON.2 – O Novo Norte, NSRF, ERDF). His current research interests include the development of DNA-based tools to track bacteria in the environment, contributing to better characterize their ecology and life style.

M.V. Mendes

Marta V. Mendes is a Biochemistry graduate (1997), University of Lisbon (Portugal) and holds a PhD in Biology (2003), University of León (Spain). Currently she is a researcher and team leader at IBMC - Institute of Molecular and Cell Biology, Porto (Portugal). Her main research interests include the study of molecular signalling in the Actinobacteria secondary metabolism.

F. Tavares

Fernando Tavares is Assistant Professor at Faculdade de Ciências, UP, and scientific coordinator of a research group on Microbial Diversity and Evolution (MDE), at CIBIO/InBIO. His main research interests are focused on culture independent DNA-based methods to trace microbes in complex environments, and to understand how selective pressures shape microbial adaptations to specific niches.