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Whole brain reconstruction from multilayered sections of a mouse model of status epilepticus

This research concerns confocal fluorescence microscopy imaging of the whole brain of C57BL/6 mice with single-cell resolution. These brains are too large for specimen holders in available 3D microscopes, so this research develops a set of volume reconstruction methods to reproduce a whole brain from multilayered, thin sections of the brain imaged using a confocal microscope. As the sections are in solution during imaging, their shapes warp differently, and their structures no longer align. The proposed two-stage reconstruction procedure consists of single-section correction and section-to-section alignment, towards producing a whole brain volume. In the first stage, the proposed method carefully unwarps the distorted shapes of each section. The second stage aligns prominent features between the layers of neighboring sections. This paper also newly considers how these stages influence each other in the broader context of whole brain volume reconstruction. Experimental results portraying each stage with real image data suggest that the proposed approach can produce consistent 3D volumes and largely correct the observed distortions.