CTF correction in Tomography

[Anindito Sen]

Dear EMAN2 Team,

During CTF estimation after tomographic reconstruction using e2spt_tomoctf.py, the Our dataset consists of whole-cell tomography, and we are not interested in performing 2D classification or averaging. Our objective is to use the CTF parameters estimated by e2spt_tomoctf.py after tomographic reconstruction to correct the individual tilt-series micrographs.

Is there a way to transfer these estimated CTF parameters back to the corresponding tilt images and apply CTF correction to the tilt series?

I would appreciate your advice on whether this is possible within the current EMAN2 workflow.

Best regards,

Andy

Texas A&M 

[Muyuan Chen]

If you run tomogram reconstruction again after CTF estimation, it will do phase flipping on the tilt series using the CTF information before reconstruction. However, it does not save the phase flipped tilt series, because they are downsampled and clipped to small tiles (each with different defocus) prior to reconstruction. It is probably not too hard to implement something that write out the corrected micrographs if you are willing to write some simple scripts…

On Nov 5, 2026, at 4:58 PM, Anindito Sen <andyse...@gmail.com> wrote:



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[Anindito Sen]

That will be good in this particular case, I am dealing with. What will be the command /script?

Regards 

[Muyuan Chen]

I think just changing the make_tomogram_tile function in e2tomograms.py program to this should work. Hopefully the attachment works.

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