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Computed alignment of serial sections for 3D reconstructions

Image alignment is an absolute requirement for creating three-dimensional reconstructions from serial sections. The rotational and translational components of misalignment can be corrected by an iterative correlation procedure, but for images having significant differences, alignment can fail with a likelihood proportional to the extent of the differences. We found that translational correction was much more reliably determined when lowpass filters were applied to the product transforms from which the correlations were calculated. Also, rotational corrections based on polar analyses of the images' autocorrelations instead of the images directly contributed to more accurate alignments. These methods were combined to generate 3-D reconstructions of brain capillaries imaged by transmission electron microscopy.