Extended Data Fig. 3: Methods of image and data analysis.

a, Images acquired from automated imaging are compiled into a large montage image. b–d, Registering multiple images using fiducials. An embryo acquired during automated imaging (b) can be automatically rotated in 3D space using ELAV (teal) as a fiducial. Once properly rotated, maximum projections of the ventral half can be computed (c). Finally, the 2-D projections can be elastically registered – or deformed – to align multiple samples (d). e–g, Methods of measuring expression patterns. (e) Sliding window analysis. A box is drawn between A2 and A3 and centred within A2. Multiple measurements are taken, sliding the box across the stripe. Each point on the boxplot represents one measurement within the box. In box plots, centre line is mean, upper and lower limits are standard deviation and whiskers show 95% CIs. (f) State method analysis. A row of cell-sized regions of interest are dragged down across the A2 stripe. Each point on the boxplot represents a single cell. (g) Plot profile analysis. A box is drawn from the A1 to A5 and the mean intensity is taken for each column of pixels and plotted (N = 10 embryos). Shaded areas indicate ± 1 SD, solid line is the mean expression. Scale bars, 100 μm. Embryos are matched to scale respectively in (a) and in (b-e), and (g).