I want to align 26 individual images, each measuring 1280x960 pixel, section thickness of 60 nm. The pixelsize
is about 30 nm.
My approach was: (modified from: https://groups.google.com/forum/#!topic/fiji-devel/FET8-Cs-qRg)
- Adjust>Image Filters `Robust Local Contrast: Standard parameters
- Least square alignment, rigide: Standard parameters
- Least square alignment, affine: Standard parameters
- Elastic alignment, rigide:
Scale of 0.5 (because of 30 nm pixelsize/ 60 nm section thickness)
Search radius 200
Block radius 100 (or should this be 200 too?)
Resolution of 35
Test 5 layers
(layers are pre-aligned checked)
The final, elastic alignment took about 5-7 hours (over night) but drastically improved the previous alignment.
The result of this workflow was “ok”, but there is still a significant moving between the individual sections.
I already used test blockmatching parameters, but I have problems to read the final image and interprete the colours.