Globally optimal stitching of tiled 3D microscopic image acquisitions

MOTIVATION: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks. RESULTS: To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem,…