Nonlinear visualisation and pixel-based alignment of 2D electrophoresis images

Abstract Data analysis at the pixel level instead of the protein spot level in the context of experiments generating two-dimensional gel electrophoresis (2DE) images requires a complete workflow description starting with an image analysis part (preprocessing and alignment), and ending with a statistical analysis. Here we describe the image analysis part of the workflow focusing on: 1) A nonlinear image intensity transformation enhancing the weaker protein signals. 2) A pixel-based 2DE image alignment method, based on a modified version of the optical flow principle. Image enhancement and alignment according to these principles was found to improve data quality in the sense that it was possible to detect a larger portion of small protein spots across 2DE gels without loss of information concerning the larger spots. Furthermore with the presented method, the volume of protein spots after alignment is kept as before alignment.