[3dem] anisotropic magnification distortion correction with mag_distortion_estimate/correct
Marin van Heel
marin.vanheel at googlemail.com
Fri Aug 14 16:03:31 PDT 2020
The normally used procedure (all with IMAGIC) would be:
convert image format to imaging: command EM2EM
camera normalisation correction, command: CAMERA-NORM-CORRECTION
calculate movie spectra from a stack of movies: MOVIE-SPECTRUM
(or a single stack of images): AMPLITUDE-SPECTRUM
(eigenvector analysis): MSA-RUN
Then select one or more eigen-spectra for the
FIND-ANISOTROPIC-MAGNIFICATION procedure
So you would never leave the IMAGIC environment!
Hope this helps,
Marin
On Fri, Aug 14, 2020 at 7:34 PM Xian, Yuejiao <yxian at miners.utep.edu> wrote:
> Hello, Marin,
>
> Thank you, the information is very helpful. One last question if I may,
> what program do you recommend to get the amplitude-spectrum eigenimage from
> the full dataset?
>
>
> Best,
> Yuejiao
>
> ------------------------------
> *From:* Marin van Heel <marin.vanheel at googlemail.com>
> *Sent:* Friday, August 14, 2020 3:24 PM
> *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
>
>
> 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!VRlNECcb9e5JQiOaEQSAWy7AkHAWRsk6LLwyzbucm8pqW1aBmlBRxy7g-JCTPSkwrA$
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> )
> [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
>
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> Afanasyev
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> C. Seer-Linnemayr
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> R. B. G. Ravelli
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> R. Matadeen
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> S. De Carlo
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> M. Schatz
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> and M. van Heel
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> )
>
> Cheers,
> Marin
>
> https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html__;!!Mih3wA!VRlNECcb9e5JQiOaEQSAWy7AkHAWRsk6LLwyzbucm8pqW1aBmlBRxy7g-JBsF0I7Aw$
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>
> [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
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