User‐friendly semiautomated assembly of accurate image mosaics in microscopy

We present a semiautomated software solution to the problem of extending the lateral field of view of a classical microscope. The initial requirements are a set of overlapping images, along with their user-provided coarse mosaic. Our solution then refines this initial mosaic in a fully automatic fashion. We rely on a highly accurate registration engine to perform the pairwise registration of the individual images, and on an efficient strategy to minimize the amount of computations while maintaining the highest possible global quality. We describe these ingredients, which we make available as a free multiplatform user-friendly software package. We also highlight why and how the specific aspects of the present microscopy application differ from those encountered while creating more common mosaics such as panoramas. Finally, we present experimental results that illustrate and validate our method on a real biological sample. We conclude by showing that we are able to reach subpixel accuracy.