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

[Marin van Heel]

Dear Yuejiao Xian

I had a quick look at your data and I noticed that you have significant
power anisotropy in your gold grating images.
It is a better idea in general to use the dataset itself rather than to get
the anisotropy from a separate measurement!
Use the water-rings in the main eigenvectors of the amplitude spectra as
per our paper.
( Single-particle cryo-EM using alignment by classification (ABC): the
structure of *Lumbricus terrestris* haemoglobin
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Afanasyev__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkoBn6lnzQ$ ,
P.>P. Afanasyev
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Afanasyev__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkoBn6lnzQ$ ,
P.>, C. Seer-Linnemayr
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Seer-Linnemayr__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkodtV9-zQ$ ,
C.>, R. B. G. Ravelli
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Ravelli__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkocok_K8Q$ ,
R.B.G.>, R. Matadeen
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Matadeen__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkr68lb68A$ ,
R.>, S. De Carlo
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=De__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkq3bxCs3g$ 
Carlo, S.>, B. Alewijnse
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Alewijnse__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkqAR_seKQ$ ,
B.>, R. V. Portugal
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Portugal__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkoe1RAjrA$ ,
R.V.>, N. S. Pannu
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Pannu__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkqC88twZg$ ,
N.S.>, M. Schatz
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Schatz__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkoSSL2u6g$ ,
M.> and M. van Heel
<https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=van__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkowF8VRnA$ 
Heel, M.> )

Cheers,
Marin

https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkoSJgSyZg$ 

[image: image.png]



On Fri, Aug 14, 2020 at 2:50 PM 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
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200814/3d1516f7/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 1583683 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200814/3d1516f7/attachment-0001.png>