Fig. 1S3

Registration workflow for in situ pattern alignment.

(A) Iterative shape averaging is used to select probe reference fish (PRF). All wild-type fish from the same age stained with the same probe (8+) are aligned in the green channel. The initial alignment is done using a rigid transform and an average fish is created from the aligned images. In the next round of registration, all embryos are aligned to the rigid average using a similarity transform. A new average is created from the aligned images and the process is repeated with an affine transform and finally a deformable B-spline transform. (B) The individual wild-type embryo with the highest correlation (max corr) to the B-spline average is chosen as the PRF. The PRF is aligned to the unstained reference fish (URF) and thereby to the anatomical brain atlas with rigid and affine transforms in the blue channel. (C) All wild-type and mutant embryos from the same age stained with the same probe are aligned to the PRF with rigid, similarity, affine, and finally B-spline transformations in the green channel.