Fig. 3

Embryo features activating the neural network.

Class activation heatmaps based on the last convolutional layer of EmbryoNet-Prime showing the part of the image that activates the network at the given timepoint for normal (a) and signaling-defective embryos (b–h). Every signaling-defective embryo (−BMP (b), +RA (c), −Wnt (d), −FGF (e), −Nodal (f), −Shh (g), −PCP (h)) is displayed in all classification channels, but only the classification channels corresponding to the correct signaling manipulation show warm colors. The percentages represent the probability of detection. See Supplementary Note 3 for sample sizes. Also see Supplementary Videos 9–24. i–k, Selected embryos showing defects highlighted by the corresponding class activation heatmaps for −Wnt at 13.4 h.p.f. (i) and −Nodal at 10.6 h.p.f. (j) and 26 h.p.f. (k). Scale bars, 500 µm.