Serial section registration of axonal confocal microscopy datasets for long-range neural circuit reconstruction

► Method for aligning axonal projections across thin histological serial sections. ► Allows for nonrigid corrections for moderate tissue deformations. ► Uses a landmark-based approach to registration that incorporates axon orientation, size, and position characteristics when assigning correspondences across sections. ► Successfully registered 5 sections of a ∼4200 μm × 5500 μm dataset with approximately 900 landmarks at each section boundary.