TrakEM2; serial section alignment, speed up and improve alignment

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I want to align 90 EM-serial sections (each measuring about 10 000 x 10 000) using Fiji/ TrakEM2. I already aligned other datasets with similar dimensions using a combination of least square alignment (first rigid, then affine) and elastic alignment (resolution 80, test maximally 10 layers). The result was really nice.

Using the same workflow (1. Coarse manual alignment, 2. Least square rigid with standard parameters, 3. Least square affine with standard parameters. 4. Elastic alignment with resolution of 80 and test maximally 10 layers), I was able to align a small amount of 5 and 10 EM-serial sections. The calculating was done in a “very short” time, only several minutes with my workstation, but it took several hours to apply the calculated parameters. The calculating for the 90 EM-serial sections took 1-2 hours, but it applies since about 2 days now.

I used the information on this website to choose the right parameters:

Can someone recommend an improved workflow to speed up the process and still have a nice alignment?
I already tried a ramdisk (only with my slow PC), but there was no big difference to the HDD. On my workstation, I use windows 10, 128 GB RAM, 16 fast Xeon Cores.
Is it possible, that black edges on the individual images slow down the process?



I was able to speed up the elastic alignment drastically using a resolution of “40” instead of “80”. Afterwards, I made a second alignment using a resolution of “55”, the result is ok, but there are still minimal misalignments (I used only rigid elastic alignment).

Perhaps, someone has an idea to improve the quality of the elasic alignment by adapting the parameters to an image size of about 10 000 x 10 000?

Best regards


I’m having the same issue. I’m trying to elastically align serial sections with large images (each 16000 x 16000). The alignment itself takes a few minutes before giving the message “Done optimizing spring meshes”. However, applying the alignment has been going for days now. Is there any way to speed up the last step? It seems like a bug.


Have you had a look at the recommendations of the author (@axtimwalde) on previous threads in the mailing lists of Fiji and ImageJ? Here you are some of them:!topic/fiji-devel/8oBdFXwivhE!msg/fiji-users/H4iO45swul0/D0nmkJvyA3gJ

I hope it helps!