3D reconstruction of brain section images for creating axonal projection maps in marmosets.

•Axonal projections were reconstructed in 3D from brain section images.•Brain section images were registered to their block-face images during sectioning.•Registration error was estimated to be <200μm.•An ICA-based autofluorescence reduction method was proposed and found to significantly improve separation of fluorescent tracer signals from the background.•The method can be combined with brain area annotation based on standard histology.