Further details of the embryo image processing and delay quantification on a single zebrafish embryo.

S5A: Single slice of 3D stack of embryo. S5B: The results of segmentation of nuclei for the 3D stack shown for this single slice. Each segmented nuclei is shown in a random colour. S5C: The notochord and embryo boundaries are manually determined for a number of slices in the 3D stack and the results interpolated throughout. S5D: The resulting slice with nuclei within the notochord, out of the embryo boundary or with too much of the nuclei touching the stack boundary removed. The remaining nuclei are those that we analyse. S5E: The slice with only the nuclei that we analyse, and only her1 mRNA transcripts that fall within these nuclei included in the image. S5F: The stack is divided into 40 intervals from the posterior of the PSM to the anterior. The gradient of the intervals are based on the gradient of the her1 mRNA waves. The frequency of nuclei with one dot and two dots is quantified for each interval. S5G: The resulting quantification of frequency of nuclei with one dot and two dots, per interval. S5H: The smoothed signals of S5G Fig. The two dot signal is clearly delayed behind the one dot signal. S5I: Comparison of automatic quantification to manual quantification for the same embryo. A manual count of the number of dots per nuclei in each interval for the innermost single slice of the embryo versus the count per interval in this slice, derived from the three dimensional quantification. The signals are similar, suggesting that the automatic quantification is accurate.