Trace driven registration of neuron confocal microscopy stacks

Active research in the area of 3-D neurite tracing has predominantly focused on single sections. Ultimately, however, neurobiologists desire to study the long range connectivity of the brain, which requires tracing axons across multiple serially-cut sections. Registration of axonal sections is challenging due to several factors, such as sparseness of the axons and complications of the sectioning process, including tissue deformation and loss. This paper investigates a method for registering sections using centerline traces which provide the locations of axons at section boundaries and the angles at which the axons approach the boundaries. This information is used to determine correspondences between two serial sections. Both global and local differences are accounted for using rigid and non-rigid transforms. Results show that utilizing information from traced axons allows axon continuity across sections to be restored.