[3dem] anisotropic magnification distortion correction with mag_distortion_estimate/correct

[Tim Grant]

Hi Yuejiao,

0.15% is not a significant result, as it changes the rings so little, so
the angle changing is likely to be a random effect. Both results are
essentially telling you that there is very little to no magnification
distortion.  A good way to confirm this is to overlay the rotationally
averaged ring with the original ring and flick between them.  If there is
appreciable distortion you should see a directional difference in the rings
(it will look like they are being squashed in one direction).  In your
case, as far as I can tell your rings line up well.

Thanks,

Tim

On Fri, 14 Aug 2020 at 12:50, Xian, Yuejiao <yxian at miners.utep.edu> wrote:

> Hello, all.
>
> I am trying to estimate the anisotropic magnification distortion from a
> cryo-EM dataset, however, I am not sure if I got the accurate estimation. I
> appreciate any comments or suggestions.  Here is what I did:
>
> I stacked about 70 gold grating images into one mrc file, which I used as
> the input of the mag_distortion_estimate program developed by Timothy Grant
> and Nikolaus Grigorieff. Here is the output parameter:
>
> =====================================
>
> The following distortion parameters were found :-
>
>
>
> Distortion Angle     = 112.6
>
> Major Scale          = 1.001
>
> Minor Scale          = 0.999
>
>
>
>  Stretch only parameters would be as follows :-
>
>
>
> Distortion Angle     = 112.6
>
> Major Scale          = 1.002
>
> Minor Scale          = 1.000
>
> Corrected Pixel Size = 0.669
>
>
>
> The Total Distortion = .15%
>
> =========================================
>  The outputted ring images are attached. The ring on the left is the
> combined ring before any distortion correction, the one in the middle is
> the rotational averaged ring, the one in the right is the ring after
> distortion correction.
>
> To verify if the parameters are accurate,  I then took the three
> parameters ( highlighted in bold) and the same stack file as an input for
> mag_distortion_correct to correct the distortion. With the corrected stack
> file, I then estimated the distortion again, and it showed the images still
> have 0.15% distortion, with the following parameters:
>
> =========================================
>
> Distortion Angle     = 21.0
>
> Major Scale          = 1.001
>
> Minor Scale          = 0.999.
>
>
>
>  Stretch only parameters would be as follows :-
>
>
>
> Distortion Angle     = 21.0
>
> Major Scale          = 1.002
>
> Minor Scale          = 1.000
>
> Corrected Pixel Size = 0.669
>
>
>
> The Total Distortion = .15%
>
> =========================================
>
> Note that the values of both major and minor scale remind the same as
> before its corrected, but the distortion angle changed dramatically. Why
> could be the reason for this? If you had experience with the
> mag_distortion_estimate/correct, would you please let me know if there is
> anything that I should specifically pay attention to in order to get the
> accurate estimation?
>
> Many thanks in advance.
>
> Yuejiao Xian
> Ph.D candidate,
> Department of Chemistry and Biochemistry,
> University of Texas at El Paso
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