Abstract
Aligning thousands of images from serial imaging techniques can be a cumbersome task. Methods ([2, 11, 21]) and programs for automation exist (e.g. [1, 4, 10]) but often need case-specific tuning of many meta-parameters (e.g. mask, pyramid-scales, denoise, transform-type, method/metric, optimizer and its parameters). Other programs, that apparently only depend on a few parameter often just hide many of the remaining ones (initialized with default values), often cannot handle challenging cases satisfactorily. Instead of spending much time on the search for suitable meta-parameters that yield a usable result for the complete image series, the described approach allows to intervene by manually aligning problematic image pairs. The manually found transform is then used by the automatic alignment as an initial transformation that is then optimized as in the pure automatic case. Therefore the manual alignment does not have to be very precise. This way the worst case time consumption is limited and can be estimated (manual alignment of the whole series) in contrast to tuning of meta-parameters of pure auto-alignment of complete series which can hardly be guessed.