A 2D quantified expression profile from a single Nematostella gene expression image. A) At the start of gastrulation, the gene Nvvas2 is expressed roughly symmetrically with respect to the blue axis drawn (image from ). B) For all points of the 3D array P, the base points S1 and S2 of the arc centered on this axis are determined. The intensity is calculated as the weighted average of these base points, as expressed in the algorithm in figure 6B. C) The greyscale intensity is displayed in three perpendicular planes of the 3D gene expression array. The horizontal plane is the truncated original. D) The primary axis is indicated on the original image. E) From the 3D expression, slices are calculated at equally incremented angles through the primary body axis. F) The original embryo geometry is overlaid on the first five pattern slices from figure 7E (the last four are identical in reverse order). As expected, the embryo geometry does not match the expression outlines. The geometry is not adjusted to the expression, because the expression representation is not meant to approach the embryo’s shape. Besides, the expression outline outside the central x,y plane is too blurred for a precise geometry extraction. (The distortion is more obvious with a dark background, as seen in Figure 5D.) G) After processing each 1D expression profile derived from the decomposed angular slices, the complete two-dimensional expression array is plotted as an intensity landscape. The cell layer position follows the segments in the decomposition in counterclockwise direction, starting and finishing at the aboral end. The angular slice designations correspond to the number labels in panel E. Processing of one-dimensional profiles is done in a similar fashion as in example 1 (main text).
Botman and Kaandorp BMC Research Notes 2012 5:555 doi:10.1186/1756-0500-5-555