I want to align/montage about 1000 single TEM-images (dataset 1) and about 4000 single TEM-images (dataset 2), using TrakEM2. These datasets are only montages, no image-stacks (just 2D datasets). The dimensions of a single image is 4084x4084 pixel (I had to crop because there were empty areas with the 4k Eagle CCD camera).
Using my new workstation, I already made very nice and homogeneous datasets, but there are few residual misalignments. I used:
Import: Via the “Layers” window-> import sequence as grid
-> Standard parameters, phase correlation, 20% overlap
Alignment: Least square with translation
-> Standard parameters
Using histogram normalization and equalisation in combination with match intensity, the result was very nice.
Can someone recommend special parameter values to adapt to such big 2D-datasets? Remaining misalignments are mostly (after phase correlation import and least square alignment) shifts between rows of about 50-100 pixel, but not between every row.
I already read several manuals about these parameters, but they seem to be optimized for image stacks (3D datasets) with only a small number of images in each layer…