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

[Xian, Yuejiao]

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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