Fig. 1: Characterization of zebrafish development with Twin Networks.
From: Uncovering developmental time and tempo using deep learning
a, Architecture of the Twin Network pipeline. b, Schematic for embryonic age prediction. A test image (top) is compared with a sequence of reference images with known temporal order (middle). The age of the test image corresponds to the age of embryo images with highest similarity (red dashed line); expectation based on absolute (gray curve) or relative (blue curve) similarity of input data. The width of the peak is indicated by green shading. c, Similarity plots between test embryos (top) and reference images (bottom). Each test embryo was compared with three reference image sets. The mean of cosine similarities to these reference sets is plotted as a datapoint for each reference image timepoint. Boxplots are based on the distribution of similarity values above 0.8. The center represents the median, box limits represent upper and lower quartiles, whiskers the 1.5× interquartile range and red points the curve maxima. Three images from the acquisition of one embryo, representative for three independent experiments, are shown. d, Schematic for prediction of embryonic trajectories. Calculation of similarities between a test embryo (top) and a reference image timeseries (bottom row) with the peak of the similarity curve corresponding to the predicted embryonic age of the test image. Bottom row, left plot shows similarity curves calculated for several test images with known temporal order of one test embryo. For each image in the test image sequence, predicted embryonic age can be calculated. The right plot shows predicted embryonic age for each image in the test image sequence plotted based on the known temporal order of the test images. e, Developmental trajectory reconstructed for one representative test embryo (n = 126, see Extended Data Fig. 3e for median of full dataset). The blue scattered datapoints show the Twin Network prediction and the red line is the expected groundtruth trajectory. Test images are shown next to the x axis, reference images are shown next to the y axis. Scale bars, 500 μm.
