Extended Data Fig. 7: Automatic detection of developmental epochs and transitions in zebrafish (Danio rerio) embryos.
From: Uncovering developmental time and tempo using deep learning
The Twin Network detects and partitions embryo development into phases that are in line with the classical zebrafish staging atlas6. The term autostage describes a time phase within the recorded developmental period of an embryo that can be delineated by a plateau of coherently high similarity values calculated using the Twin Network. These similarity values were calculated by self-similarity comparison with images of previous developmental stages of the same test embryo. (a) Automatically selected images at the beginning, in the middle, and at the end of Twin Network-predicted plateaus of similarity values, that is autostages, for one test zebrafish embryo (embryo 1). Embryos for illustration in (a) also shown in Fig. 5b. (b) Calculated similarities used as the basis for the selection of depicted images of embryo 1. (c) Time points in the classical staging atlas6 are shown at the top. Automatically generated autostages were calculated based on phases of high similarity in embryo morphology and are shown below. Embryos for illustration in (c) also shown in Fig. 5b. (d) Automatically selected images based on autostages as described in (a) for a zebrafish embryo (embryo 2). (e) Calculated similarities used as the basis for the selection of the depicted images of embryo 2. (f) Time points in the classical staging atlas6 are shown at the top. Autostages were calculated based on phases of high similarity in embryo morphology and are shown below. (g) Automatically selected images based on autostages as described in (a) for a zebrafish embryo (embryo 3). (h) Calculated similarities used as the basis for the selection of the depicted images of embryo 3. (i) Time points in the classical staging atlas6 are shown at the top. Autostages were calculated based on phases of high similarity in embryo morphology and are shown below; n = 3 out of 131 representative embryos. Images in (a), (d) and (g) correspond to the pictograms in (c), (f) and (i) at the indicated timepoints. The reference stages in the upper panels of (c), (f) and (i) are annotated with the time postfertilization (min). The example images in (a), (d) and (g), the similarities in (b), (e) and (h), and the autostages in the lower panels of (c), (f) and (i) are annotated with the experimental time (min). Imaging was started at 2 hpf (64-cell stage). Scale bars, 500 μm.
