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Fig. S1
Preprocessing steps to automatically detect, segment and track fluorescently labeled nuclei in light-sheet microscopy images of a zebrafish embryo.
(A) Maximum intensity projection of a single time point of an entire zebrafish embryo at early somitogenesis stages [11, 66]. (B) Maximum intensity projection of a 3D light-sheet microscopy image with superimposed centroids of detected cell nuclei in red. (C) Volume rendering of segmented cell nuclei using a random color code. (D) Exemplary movement paths for 25 arbitrarily selected neural crest nuclei of a zebrafish embryo that were automatically tracked using a nearest neighbor algorithm [58, 59]. Dorsal view of the anterior half of the embryo (anterior up). All data sets were aligned prior to the analysis, to obtain a common reference orientation. (E) Whole-embryo data sets were oriented such that the animal-vegetal axis was aligned with the y-axis (animal pole on the positive y-axis) and the dorsoventral axis was aligned with the x-axis (dorsal part on the positive x-axis). (F) The embryos highlighting neural crest cells were oriented such that the anteroposterior axis formed a left-right symmetry axis with the head region on the positive y-axis (dorsal view, anterior up). Circled regions in (F) indicate the positions of the prospective eyes and the olfactory epithelium of the embryo, respectively. The green rectangle in panels (A) and (E) indicates the neural crest cell region visualized in (F). Panels (A)-(D) were adapted from [67] and panel (E) was adapted from [11]. Scale bar: 100 μm.