Test block matching parameters

[rtas]

Hello,

I have serial histological sections that i want to elastically align.
I aligned the images rigidly first. Based on these images, I have used Test
block matching parameters to two continuous sections to see whats the best
parameter for elastic alignment (see the images for the result).
I refer this page (http://wiki.imagej.net/Test_Block_Matching_Parameters)
how to improve the parameter. but i am not quite sure how to interpret the
result.
What kind of color am i supposed to get if the parameters are correct?
Is the color of this result the systemic one? What is non-systemic random
colors?

I applied the same parameters to align 25 images. I see the elastic
transformation of the images however, the most deformed parts of images
[these are lower part of images, such as circular shaped blue stained
regions and the oral spaces surrounded by epithelial tissues just above the
those blue stain regions] that i want to align  are not aligned well
enough.

Which parameter should i change to align the more deformed regions?


I appreciate any suggestion!


Thank you,

Rui

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