Morphology registration pipeline

After the slices have been aligned and the pieces of neurite have been stitched together in a single valid neuron, the neuron registration pipeline is used to warp the neuron to a common reference space. The strategy to follow depends a lot on the usecase, in particular on whether the slices have been badly deformed in shape or contrast.

In the collab morphology-atlas-registration-v2 we present a usecase in which the sections of a neuron are not good enough to be automatically registered into a 3d volume. Instead, each section is first roughly registered to the Allen Mouse refertence space CCF3 using QuickNii, and then the Elastix package is used for additional nonlinear warping. Registering each section individually does come at a price: the resulting neuron has discontinuities. These are resolved by finding the best possible linear transform between the original neuron and the registered neuron. This linearly warped neuron is then used as the end result.