Biochemistry Publications


Automatic detection of noisy spots in two-dimensional Southern blots. International Electrophoresis Society Meeting, Washington DC, March 16-19, 1991.

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Applied and theoretical electrophoresis : the official journal of the International Electrophoresis Society





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One of the problems of automatically quantitating 2D DNA gels, is clearly detecting spots visualized by Southern hybridization blots using DNA probes (Rogan et al. in this conference). Spots appear noisy due to multiple transfer steps. If one applies standard 2D PAGE protein gel spot segmentation methods, spots fragment due to highly textured image noise and a weak radioautograph signal and thus are poorly detected. We have observed that these spots are all of a minimum size. Therefore an image processing filter which both takes minimum spot size into account and has immunity to image texture-type noise should be able to reliably detect this class of spots. The 'Busse' Laplacian filter used in the GELLAB-II system, is a modification of the standard (1-21) digital approximation of the Laplacian. In the Busse Laplacian, the sampling interval is n pixels (n greater than 1) instead of 1. In addition, 3 x 3 averaged 'super pixel' values are used instead of single pixels for each element of the Laplacian convolution. This gives the needed noise immunity by filtering out the high spatial frequency image noise while preserving the low spatial frequency character of the spots. We have used this filter successfully on 2D DNA Southern blot image data.

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