The ways in which embryo development can vary across individuals of a population determine how genetic variation translates into adult phenotypic variation. The study of developmental variation has been hampered by the lack of quantitative methods for the joint analysis of embryo shape and the spatial distribution of cellular activity within the developing embryo geometry. By drawing from the strength of geometric morphometrics and pixel/voxel-based image analysis, we present a new approach for the biometric analysis of two-dimensional and three-dimensional embryonic images. Well-differentiated structures are described in terms of their shape, whereas structures with diffuse boundaries, such as emerging cell condensations or molecular gradients, are described as spatial patterns of intensities. We applied this approach to microscopic images of the tail fins of larval and juvenile rainbow trout. Inter-individual variation of shape and cell density was found highly spatially structured across the tail fin and temporally dynamic throughout the investigated period.

Images & landmarksMicroscopic images of the tail fins of 20 rainbow trout specimens (Oncorhynchus mykiss). The fish were collected from one hatchery in the year 2000. Specimens were euthanized by overdose of MS222, fixed in buffered formalin, and stored in 70% ethanol. Seven of them were fixed at 21 days post fertilization (dpf), eight at 40 dpf, and five at 56 dpf. In 2013, the specimens were transferred into distilled water before they were stained with Mayer’s hematoxylin for 10 minutes. All images were taken under identical light conditions and standardized specimen orientation with a 5x magnification. Four anatomical landmarks and 95 semilandmarks were recorded on each of the 20 images using the software TPSdig (James Rohlf). The resulting raw landmark coordinates are given in the file "landmarks.tps".Images_landmarks.zip