Correcting lamella pre-tilt after autoalign_dynamo alignment

[Peng Liu]

Dear all,

I aligned a tilt series using autoalign_dynamo with fiducials, and the
alignment looks very good based on the residue values. Since the
tomogram is from a lamella, it has a 14–15° pre-tilt from FIB milling,
and I would like to correct this. As far as I know, AreTomo cannot
read the .xf file generated by autoalign_dynamo.

Because IMOD GUI cannot directly import this .xf file, I used newstack:

newstack -input unalignedstacks.st -output dynamo_aligned.st -xform align.xf

The resulting stack appears well aligned. I am now considering how to
correct the pre-tilt:

Option 1: Use newstack to generate or reorder the angle file (I saw
some relevant flags, but I need to understand how to use them
properly). Then reconstruct the tomogram using newstack or Warp (which
can read .tlt files).

My concern is whether this approach would affect downstream STA
analysis. In particular, if frame files are needed later, I am unsure
whether I would also need to rename the frame files and modify the
tilt angles in the .mdoc files to keep everything consistent.

Option 2: Start from the frames data and manually rename frame files
and modify the .mdoc tilt angles to include the pre-tilt correction
from the beginning.

I am not sure which approach is correct, or whether there is a better
way. I would greatly appreciate any guidance or suggestions.

Best regards,

Peng

[Alister Burt]

Hi Peng,

Dimitry added a new ts_autolevel command to warptools recently, I’m not sure a conda package has been built including this yet but you could try to build from source and run that :-)

I’m travelling but you should be able to find instructions for building on Linux in the GitHub issues somewhere… I really should write a docs page for that.

Cheers,

Alister

Sent from mobile - apologies for brevity

> On Nov 17, 2025, at 12:45, Peng Liu <penggr...@gmail.com> wrote:
>
> Dear all,

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[Hamidreza Rahmani]

Hi all,

I am on   2.0.0dev36 and I see the ts_autolevel when I run ts_import_alignment. But I have never tried using it. At the moment we edit our mdoc files before making stacks to flatten the tomo.

Best,

Hamid

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[Hamidreza Rahmani]

Sorry I meant when I run WarpTools!

[Alister Burt]

Thanks Hamid! tilt angle editing means you’re only correcting one axis, the autolevel program will completely flatten the sample :-)

Sent from mobile - apologies for brevity

On Nov 17, 2025, at 16:48, Hamidreza Rahmani <hami...@gmail.com> wrote:



[Peng Liu]

Dear Alister,

Thank you very much for your information. It sounds exciting that we have this new function now. It is exciting to hear that this new function is now available and can flatten all axes. Building a package is new to me, but I would be happy to explore it as you suggested.

As Hamidreza mentioned in a separate email, the ts_autolevel function was also spotted in WarpTools, and I will take a look at that as well.

Have a nice trip,

Peng

--

Dr. Peng Liu

Max-Planck-Institut für biophysikalische Chemie
Am Faßberg 11, 37077 Göttingen
Germany

 : +49(0)17635209768
Email: peng...@mpibpc.mpg.de