[3dem] Fixing pre-alignments

Bill & Sue Tivol wtivol at sbcglobal.net
Wed Nov 5 17:39:24 PST 2014

On Nov 5, 2014, at 4:49 AM, Mike Strauss wrote:

> once you fix the alignment in Midas, and save the transformations,  
> you just need to rerun “Generate Course Aligned Stack” ( think  
> that’s what it’s called).  Do NOT run the automatic correlation step  
> again, as that will overwrite your Midas work.
> As I understand it, the process is as follows:
> -find frame-to-frame transformations (either by correlation or by  
> Midas) - these are saved as a .xf file
> -calculate the global transformations (to retain the majority of the  
> image in the frame) - using xftoxg
> -apply global transformations to the unaligned stack
> Etomo takes care of the second two steps at once with the “Generate  
> Course Aligned Stack” button.
> If you want to try to get better initial automated alignment, it may  
> be worth trying any (combination) of the following:
> in the advanced tab:
> Click Exclude central peak
> Change frequencies used
> Try No Cosine Stretch
> Try Cumulative correlation
> I’ve had some luck with some of these in the past, but it does  
> depend on your data set.
Hi Ariane, Huy, Lu, & Mike,
	Thanks for your responses.  I think my error was rerunning the cross- 
correlations.  I put in Mike's response, since it was the most  
complete.  Thanks also for the suggestion of the IMOD list; I didn't  
know there was one.

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