Automated high speed stitching of large 3D microscopic images

High-resolution microscopic imaging of biological samples often produces multiple 3D image tiles to cover a large field of view of specimen. Usually each tile has a large size, in the range of hundreds of megabytes to several gigabytes. For many of our image data sets, existing software tools are often unable to stitch those 3D tiles into a panoramic view, thus impede further data analysis. We propose a simple, but accurate, robust, and automatic method to stitch a group of image tiles without a priori adjacency information of them. We first use a multiscale strategy to register a pair of 3D image tiles rapidly, achieving about 8∼10 times faster speed and 10 times less memory requirement compared to previous methods. Then we design a minimum-spanning-tree based method to determine the optimal adjacency of tiles. We have successfully stitched large image stacks of model animals including C. elegans, fruit fly, dragonfly, and mouse, which could not be stitched by several existing methods.