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

Fri Aug 14 15:24:41 PDT 2020

Once you have an amplitude-spectrum eigenimage from the full dataset with
clear water rings like the one in the image,
You copy that out of the dataset and apply (COMMAND: MASK-IMAGE) a
ring-mask letting the environment of the water ring pass though.
The use the command FIND-ANISOTROPIC-MAGNIFICATION that gives you an output
almost identical to what you showed earlier.
the command: ANISOTROPIC-MAGNIFY-IMAGE will then correct your full dataset.
The anisotropic correction  must be applied prior to the
CTF2D-FIND-PARAMETERS command so that anisotropy will not be confused with
astigmatism... You can then proceed with CTF2D-FIND-PARAMETERS;
CTF2D-FLIP-PHASES and ALIGN-MOVIE-FRAMES, PICK-PARTICLES, etc

Hope this helps,
Marin

(https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2017/05/00/kf5002/kf5002.pdf__;!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I10wNZptA$ )
[image: image.png]

On Fri, Aug 14, 2020 at 5:30 PM Xian, Yuejiao <yxian at miners.utep.edu> wrote:

> Hello, Marin,
>
> Thank you for your quick response. I read your paper, and now I understand
> why we shouldn't use the anisotropic magnification estimation from a
> separated measurement. I will look into the water rings in my dataset.
> Please excuse me for not having much experience with IMAGIC-4D, would you
> please explain more specifically on how the anisotropic magnification
> distortion is measured from the water rings and corrected in IMAGIC-4D?
>
>
> Best,
> Yuejiao Xian
>
> ------------------------------
> *From:* Marin van Heel <marin.vanheel at googlemail.com>
> *Sent:* Friday, August 14, 2020 11:34 AM
> *To:* Xian, Yuejiao <yxian at miners.utep.edu>
> *Cc:* 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>; Yuejiao Xian <
> xianyuejiao at gmail.com>
> *Subject:* Re: [3dem] anisotropic magnification distortion correction
> with mag_distortion_estimate/correct
>
> 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://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DAfanasyev*2C*2520P.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=B*2FOZQY12839MrPCFaMs7iQFYFZp9ISeIqKl4FbXUbZI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I3RjNwwBg$ > P.
> Afanasyev
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DAfanasyev*2C*2520P.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=B*2FOZQY12839MrPCFaMs7iQFYFZp9ISeIqKl4FbXUbZI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I3RjNwwBg$ >,
> C. Seer-Linnemayr
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DSeer-Linnemayr*2C*2520C.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=rXnLF76nGQg7Bp2AJkLAf2FpMdT9VsPjQWt7fZhLh3I*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I30_T3UGw$ >,
> R. B. G. Ravelli
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DRavelli*2C*2520R.B.G.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=TiP8EhhDCOfHRD2JqA7wah*2BpsZrxhGybnBtvcIG1xGA*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I26fEzFog$ >,
> R. Matadeen
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DMatadeen*2C*2520R.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=*2B5n*2FImpIH3VyQL*2F61vl1AHql5SOTFBgxi5nd3jtQPWY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I1Xh0tGgQ$ >,
> S. De Carlo
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DDe*2520Carlo*2C*2520S.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=tMsvnrA0DUqjopvUrQANxaLQbf41Tvy*2F8fxIsP7pVU8*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I2IGn7NGQ$ >,
> B. Alewijnse
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DAlewijnse*2C*2520B.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=HXJ865N*2FqkVjSYsR0qtW4nhrZHLWuMXcuqRwoenUzUY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I3n-8zDQQ$ >,
> R. V. Portugal
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DPortugal*2C*2520R.V.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=siaDFlLRuBHt9R*2FSjlNQ5vQdtMclAAHgtf6k5ZJpjOI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I2eXdyIYg$ >,
> N. S. Pannu
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DPannu*2C*2520N.S.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=vF96R8xSbP64iln7Bq8i*2FznYmLiphhkXqzHu80vxsLM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I1FR0e8Mg$ >,
> M. Schatz
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DSchatz*2C*2520M.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=hXF5*2B*2BrPyBLvYyD2Fbxo5yyZWFRQ8Bx1dTjyFQE0PXk*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I3gHpKLQQ$ >
> and M. van Heel
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3Dvan*2520Heel*2C*2520M.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=WzrD9tHHWU6f18N2qNLfTUeUa1DYEg5wYWR8T9f4iVc*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I3o4l920A$ >
> )
>
> Cheers,
> Marin
>
> https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html__;!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I1DuRqsbg$ 
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fjournals.iucr.org*2Fm*2Fissues*2F2017*2F05*2F00*2Fkf5002*2Findex.html&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=Up1qs4p8vHdnq*2FBYmAxII67iNiSP4QLxzWfnAMJBCPE*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I0vKOdsUw$ >
>
> [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
> <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fmail.ncmir.ucsd.edu*2Fmailman*2Flistinfo*2F3dem&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=u1X9XSlt0rNXEFYJVKys6NMuK7WfTQk3S0hbmcF9hr4*3D&reserved=0__;JSUlJSUlJSUlJSUlJQ!!Mih3wA!VUV_TQV90op7U_nXen4anKY0OggtfZBoZIH3ve015zsVOosoZzr-DDXS9I12eoW2XA$ >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200814/e958d6db/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/e958d6db/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 445178 bytes
Desc: not available
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200814/e958d6db/attachment-0003.png>