Hi guys,

So I have been playing around a bit with using CMTK to register a sample that has been imaged from two sides to itself.  By then adding the signals together the weak signal I get from te middle of the tissue will be a bit stronger and hopefully be better for final analysis. The main set-up works but I am still struggling a bit with the warp settings. Though most of my cells are overlaying almost perfectly there still appear to be a few cells where the two channels are not overlapping the way they should, leading to an overestimation of the cell size when finally adding the signals. I have attached an example image(green and red are the two channels to be registered, in yellow is the sum of the two).

Right now i am running the Cachero Ostrovsky registration parameters. I have been looking at some possible things to optimize the warping settings but I a having some trouble understanding the details for the warping ( as described in on http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_parameters)

As far as i understand the solution would be to increase the number of grid refinements and the accuracy but i am not too sure. 

I would greatly appreciate if you guys could give some feedback on which parameters to change.


Best,

Pieter