http://imagej.273.s1.nabble.com/Elastic-layer-alignment-in-TrakEM2-problem-with-correspondences-tp5013279p5013294.html
> Hello everybody,
>
> my name is Klaus, I'm a PhD student from Erlangen (Germany) and am currently working on reconstructing a TEM series. The picture aquisition is not complete yet, but I already have pictures of 108 slices with roughly 8 pictures per slice. I successfully entered about 60 layers by now, montaged them (elastically) and got decent results for each layer per se.
>
> I encountered problems with the automatic alignment of layers though. So far I have tried both linear and elastic alignments for subsets of these 60 layers with varying numbers of layers compared simultaneously (3-10), varying sizes for feature extraction (min 50-2500; max 600-5000), varying search and block radii (500-2000), varying alignment errors (50-400) but so far no luck.
>
> The biggest problem that I can see is that my layers are always spaced more than usual because I only captured images from every fifth slice or so (with slight variations), due to the immense size of the project (I presum it to end at roughly 200 layers in the end). Therefore I believe the similarities from two adjacent layers are too little for the standard alignment parameters. I believe that I need to define more global features and set a different error value still.
>
> Can anyone help me with the tuning of this process or tell me that my series can or cannot be aligned automatically from what I've posted her?
>
> On a side note, the individual images were taken at an 3150x magnification and are all LZW compressed tif files with a resolution of 4008x2672. The canvas size I got from the autosize function at the moment is 18983x8910 (if that helps in any way). Also I'd like to note that I am quite the novice at this.
>
> Thank you in advance.
>
> Greetings,
> Klaus
>
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