Re: Elastic layer alignment in TrakEM2 - problem with correspondences

Posted by Saalfeld, Stephan on Jun 26, 2015; 2:02pm
URL: http://imagej.273.s1.nabble.com/Elastic-layer-alignment-in-TrakEM2-problem-with-correspondences-tp5013279p5013316.html

No---you only need a rough estimate of what the ratio between z-spacing
and xy-resolution is.  Starting from there, you can do educated search
in parameter space which usually means trying 10--20 things---not too
bad.  Without even a rough idea that becomes Kaffeesatzleserei.

Cheers,
Stephan



On Fri, 2015-06-26 at 04:24 -0400, Klaus Griebel wrote:

> Hi Stephan,
>
> I haven't calibrated the series yet. I thought it would be nicer/easier to do after I've put in all layers I want and pre-aligned them.
>
> I measured the pixel size though, it is at 0.012738854µm/px-edge (i.e. 1px= 0.012738854µm x 0.012738854µm). Also I haven't typed in all layer distances yet, as we've encounterd "problems" during the cutting process. Basically there was a mixup and I have to determine the distance for every section anew, which I haven't done yet.
>
> So are you indicating that the elastic alignment can't/won't work without the spacing data? So far I've evenly spaced the layers by 0.25µm as a "placeholder".
>
> I have actually found the Test Block Matching Parameter Plugin, but so far have been a little overwhelmed by what to do to get it to work, but it appears I need to first pre-align my series and that I had to do by hand so far. Even the linear layer alignment did not work properly so far, hence I bet I'll have to calibrate, don't I :)
>
> Thanks,
> Klaus
>
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