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Biological Image Processing

Images are becoming ubiquitous in biological applications. Current image data volumes in biology labs no longer allow traditional visual analysis, and with the increasing use of high-throughput experiments there is a pressing need for robust, reusable biological image processing tools.

We have developed tools for the analysis of biological images based on the concept of local phase. Phase-based methods have the advantage over traditional intensity-based ones that they are less sensitive to local variations in image contrast, making them particularly suited to the analysis of biological / microscopy images. In particular, we have developed tools for the extraction of networks from images, for which we have proposed a novel branch detector (the Phase Congruency Tensor) and an efficient method to extract complete networks with thousands of branches based on the watershed transform. In collaboration with Dr. Mark Fricker, from the Department of Plant Sciences, we have applied this framework to the extraction of fungal networks.

Open-source code for the Phase Congruency Tensor and related methods can be found in Dr Boguslaw Obara's web page. Boguslaw is now a Lecturer at the School of Engineering and Computer Sciences, University of Durham.

Representative Publications (see also laboratory full publication list):

Boguslaw Obara, Mark Roberts, Judith Armitage and Vicente Grau, Bacterial cell identification in Differential Interference Contrast microscopy images. BMC Bioinformatics, accepted for publication, 2013

Obara B, Grau V, Fricker MD. A bioimage informatics approach to automatically extract complex fungal networks. Bioinformatics. 2012 Sep 15;28(18):2374-81.

Obara, B., Fricker, M., Gavaghan, D., Grau, V., Contrast independent curvilinear structure detection in biomedical images, IEEE Transactions on Image Processing 21(5):2572-2581, 2012.

B. Obara, M. Fricker, and V. Grau, Coherence enhancing diffusion filtering based on the Phase Congruency Tensor, in Proc. IEEE International Symposium on Biomedical Imaging, Barcelona, Spain, May 2–5, 2012

B. Obara, V. Grau, Local phase approaches to extract Biomedical networks, in Proc. IEEE International Symposium on Biomedical Imaging, Barcelona, Spain, May 2–5, 2012