using tomogram generated by AreTomo

[jychoi0616]

Hi Tim-Oliver and Thorsten,

This is more a question rather than a issue, but thought it would be helpful to write here for others as well.

I am now using AreTomo to generate tomograms, and the AreTomo output files don't include all the etomo output files listed in your previous python script to generate even/odd frame tomogram .

Now, my question is whether it's okay to generate EVN/ODD tomograms using AreTomo using the same parameter I used for full frame tomogram. Otherwise, what would you suggest? I don't have access to warp yet because we don't have a window workstation.

Cheers, Joy

[bwmr]

Hi Joy,

In my workflow, I am also using AreTomo-aligned tomograms for cryoCARE denoising. The routine is MotionCor2 alignment with -Splitsum 1 -> AreTomo alignment of the "main" tiltseries -> applying the same transformations (saved in the .aln output) to the EVN/ODD stacks with the flag -AlnFile ts.aln -> reconstruction and trimming using imod's tilt. In my experience, this works quite nicely. I have a Python script which makes this all relatively convenient. Let me know if this would help you.

Hope this helps, Benedikt

[thorstenwagner]

I would be interested :-) Please share it.

06.10.2022 15:46:36 Benedikt Wimmer @.***>:

Hi Joy,

In my workflow, I am also using AreTomo-aligned tomograms for cryoCARE denoising. The routine is MotionCor2 alignment with -Splitsum 1 -> AreTomo alignment of the "main" tiltseries -> applying the same transformations (saved in the .aln output) to the EVN/ODD stacks with the flag -AlnFile ts.aln -> reconstruction and trimming using imod's tilt. In my experience, this works quite nicely. I have a Python script which makes this all relatively convenient. Let me know if this would help you.

Hope this helps, Benedikt

— Reply to this email directly, view it on GitHub[https://github.com/juglab/cryoCARE_pip/issues/26#issuecomment-1270081262], or unsubscribe[https://github.com/notifications/unsubscribe-auth/AAIP66JC5MR77OXZHIRBOZLWB3J3XANCNFSM6AAAAAAQDEV5Z4]. You are receiving this because you are subscribed to this thread.[Verfolgungsbild][https://github.com/notifications/beacon/AAIP66NFOZ27RN2L5ME3UPDWB3J3XA5CNFSM6AAAAAAQDEV5Z6WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTSLWPTO4.gif]

[bwmr]

Hi @thorstenwagner,

You can find the full scripts here, currently only in the branch refactoring, but we will merge it into main soon.

To go from tif-lzw frames to EVN/ODD reconstructions, you need just two commands:

1. tomotools batch-prepare-tiltseries --splitsum --gainref frames/CountRef_XXX.dm4 ts*.mrc output-dir to run MotionCor2 on all specified files (here ts*.mrc) and create the sorted stacks output-dir/ts_xx.mrc,output-dir/ts_xx_EVN.mrc and output-dir/ts_xx_ODD.mrc.
2. tomotools reconstruct --move --do-evn-odd output-dir/*.mrc to move all tiltseries (incl. EVN/ODD) to their own subdirectories, align them with AreTomo, dose-filter with mtffilter and reconstruct with tilt.

I also wrote a small function to automatically extract training data for cryoCARE from the folder structure tomotools generates (tomotools cryocare-extract).

Please let me know should you encounter any issues! Cheers, Benedikt

I would be interested :-) Please share it. 06.10.2022 15:46:36 Benedikt Wimmer @.**>: … Hi Joy, In my workflow, I am also using AreTomo-aligned tomograms for cryoCARE denoising. The routine is MotionCor2 alignment with -Splitsum 1 -> AreTomo alignment of the "main" tiltseries -> applying the same transformations (saved in the .aln output) to the EVN/ODD stacks with the flag -AlnFile ts.aln -> reconstruction and trimming using imod's tilt*. In my experience, this works quite nicely. I have a Python script which makes this all relatively convenient. Let me know if this would help you. Hope this helps, Benedikt — Reply to this email directly, view it on GitHub[#26 (comment)], or unsubscribe[https://github.com/notifications/unsubscribe-auth/AAIP66JC5MR77OXZHIRBOZLWB3J3XANCNFSM6AAAAAAQDEV5Z4]. You are receiving this because you are subscribed to this thread.[Verfolgungsbild][https://github.com/notifications/beacon/AAIP66NFOZ27RN2L5ME3UPDWB3J3XA5CNFSM6AAAAAAQDEV5Z6WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTSLWPTO4.gif]