Figure 6—figure supplement 1.

(A–C) Maximum z-projections of a two-color sample showing the lyn-EGFP membrane marker (A), the pea3 smFISH probe (B), and the results of automated spot detection with red rings denoting detection events (C). Scale bars: 10 µm. (D) Zoomed view of the region in the yellow box in (C). Scale bar: 2 µm. (E) pea3 smFISH spot counts for each cell, both from measured data (blue) and from predictions across the entire atlas dataset (purple). The left shows averages across primordia, which closely match those reported previously based on a different spot counting method (Durdu et al., 2014). The individual cell counts on the right show that there is a long tail of cells with extremely high counts, which as one would expect is not captured in the SVR predictions. (F–H) Comparisons of three important cell shape variables between fixed smFISH samples and live samples (here the set of live samples containing only the membrane label; N = 24, n = 2310), showing no significant difference.