CTFFIND Anisotropic Mag Correction - Movie Frames

Hello all,

Should the input pixel size for ctffind when using the stretch-only anisotropic magnification correction parameters be that of the uncorrected input pixel size or should it be the pixel size after mag correction using stretch-only parameters?

As of now, I am assuming it is the nominal pixel size of the uncorrected input images, and then if the pixel size is changed during mag distortion correction in ctffind using stretch-only parameters, this is passed on to the rest of the program.

Thanks for your help!


If you have corrected the mag distortion on the movies, or images before the CTF estimation (as you should do, or you would have to then correct the defocus parameters) using stretch only parameters, then you need to use the corrected pixel size as the pixel size for ctffind.

BTW, I don't know if you have tried it, but we have new software called cisTEM (www.cistem.org). This allows for magnification distortion correction, and will track the pixel size changes for you.



In reply to by timgrant

Hi Tim,

Thanks for the quick reply!

I am actually using the ctffind software that came with cistem. However, I am working with helical particles so I haven't used the full cisTEM pipeline yet. I would definitely love to use it at some point, if helical processing will become integrated in the future? :)

In the ctffind I am using, there is an option in the expert options to correct the mag distortion during ctf estimation. Therefore, I am inputting uncorrected movie frames to ctffind and letting it correct anisotropic mag internally. So since the mag correction is done internally, I am still left wondering if the pixel size I tell ctffind should be that of the uncorrected input or the resulting pixel size from the internally corrected frames? I am assuming the former.

Is the question clear? Sorry for any confusion and thanks for the help!

In reply to by davboyer

Aah I see. I thought that since you were not posting on the cisTEM forum, you were using the old programs.

The option "Correct Movie Mag. Distortion?" in ctffind should only be used if you want to give an uncorrected input, but get the results for the corrected movie. This is basically used by the GUI pipeline as it does correction on the fly, and never writes out the frames. That means that if you answer yes here, you should be giving the uncorrected frames, and the original pixel size. The output in this case will be for the corrected frames, and corrected pixel size.

If you have magnification distortion corrected movies, then you should say no to "Correct Movie Mag. Distortion?", and give the corrected pixel size.

Does that make sense?