I am trying to compare IHC staining patterns of 4 different biomarkers on whole mount slices containing tumor and non-tumor tissue. At the moment, I am working on automatically aligning the 4 consecutive sections for each slice.
Which uses these alignment functions:
autoAlign(serverBase,serverOverlay,registrationType,affine,20) autoAlign(serverBase,serverOverlay,registrationType,affine,10) autoAlign(serverBase,serverOverlay,registrationType,affine,5)
(side note: what does the last input variable (20, 10, 5) mean here?)
The script works fine, but the results of the automatic image alignment are not that great, probably due to internal deformation within the tissue. I find that the manual alignment, in which you can roughly pre-align the images, gives a better result.
Does anyone have any tips on how to improve the alignment? Is there for example a way to focus the alignment on a specific part of the image? I am mainly interested in the tumor, so as long as that part of the image is aligned, it doesn’t matter too much if the surrounding tissue is not.
Or is it maybe possible to half-automate the process, in which I can still provide the manual pre-alignment as input?
Any tips are greatly appreciated!