The display artefact was solved in the latest beta version of relion-2.0
(I hope).
S
> Hi Weiwei,
>
> We had similar issues. It's a display artefact. Open the micrograph with
> e2display.
>
> Cheers
>
> paolo
>
> 2016-10-14 2:27 GMT+02:00 Weiwei Wang <[log in to unmask]>:
>
>> Right it seem not likely related to motion correction. Though, since
>> the
>> '-Crop' option corrected the problem I think it is less likely to be due
>> to a rotation/flip mismatch of the gain reference.
>>
>>
>> I am attaching 3 screen shots (all low pass filtered at 20A):
>>
>>
>> The images in "rect-sqr.jpg" was acquired with the correctly
>> rotated/flipped gain reference. On the left is the original sized
>> rectangular image and on the right is the cropped square image (by using
>> '
>> -Crop 7420 7420' option).
>>
>>
>> The images in "rect-sqr-wrngr.jpg" was obtained with incorrectly
>> oriented
>> gain reference ( also rectangular on the left and square on the right).
>>
>>
>> The last image 'rect-unblur.jpg' is the rectangular image corrected
>> using
>> "unblur_openmp_7_17_15.exe" (
>> "mag_distortion_correct_openmp_8_18_15.exe" was
>> used to apply gain reference).
>>
>>
>> The vertical lines in the rectangular micrographs look different from
>> the
>> stripes resulting from a misaligned gain reference I think. An
>> interesting thing, if I do not use low-pass filtering for display
>> (relion, set scale 1.0 and low pass filtering 0), these lines seem to
>> disappear. When processed with
>> "mag_distortion_correct_openmp_8_18_15.exe"
>> and "unblur_openmp_7_17_15.exe", these lines seem not presence even with
>> low-pass filtering. Maybe there is some difference in how gain reference
>> is used or the low-pass filtering (fourier cropping?) process?
>>
>>
>> Thanks a lot!
>>
>>
>> Weiwei
>>
>>
>> ------------------------------
>> *From:* Shawn Zheng <[log in to unmask]>
>> *Sent:* Thursday, October 13, 2016 6:18 PM
>> *To:* Weiwei Wang
>> *Cc:* [log in to unmask]
>> *Subject:* Re: [ccpem] Fw: [ccpem] MotionCor2
>>
>> At this point we can conclude these lines are not caused by motion
>> correction. I just saw Zongli's email and think he is very likely
>> correct.
>> One more thing to try, generate uncorrected sum without gain correction.
>> This can be done by not specifying "-Gain". Again use "-Align 0" to
>> disable
>> motion correction. Compare this image and the gain reference to check
>> the
>> orientation.
>>
>> Best
>> Shawn
>>
>> On Thu, Oct 13, 2016 at 3:01 PM, Weiwei Wang
>> <[log in to unmask]
>> > wrote:
>>
>>>
>>> ------------------------------
>>> *From:* Weiwei Wang
>>> *Sent:* Thursday, October 13, 2016 5:59 PM
>>> *To:* Shawn Zheng
>>> *Subject:* Re: [ccpem] MotionCor2
>>>
>>>
>>>
>>>
>>> Hi Shawn,
>>>
>>>
>>> Both the uncorrected (-Align 0) image and the 20A low-pass filtered
>>> gain
>>> reference have the lines. Maybe it is simply due to
>>> low-pass filtering? Seems somehow the images are scaled a bit
>>> differently
>>> also? Thanks a lot!
>>>
>>>
>>> Best,
>>>
>>> Weiwei
>>>
>>>
>>> ------------------------------
>>> *From:* Shawn Zheng <[log in to unmask]>
>>> *Sent:* Thursday, October 13, 2016 3:41 PM
>>> *To:* Weiwei Wang
>>> *Subject:* Re: [ccpem] MotionCor2
>>>
>>> Try to generate uncorrected sum using -Align 0 and see if you can
>>> duplicate these lines. If yes, we may need to look into individual
>>> frames
>>> and the gain reference. Also, try low-pass filter the gain reference to
>>> 20A
>>> and see if you can see these lines too.
>>>
>>> If these tests cannot duplicate these lines, I then need your stacks
>>> and
>>> gain reference to check by myself.
>>>
>>> Best
>>> Shawn
>>>
>>> On Thu, Oct 13, 2016 at 12:16 PM, Weiwei Wang <
>>> [log in to unmask]> wrote:
>>>
>>>> Hi Shawn,
>>>>
>>>>
>>>>
>>>> The lines seems to be in the summed micrographs (instead of Fourier
>>>> transform). The gain reference was flipped / rotated before using
>>>> MotionCor2 and it seems to be OK in other programs. I am attaching an
>>>> screen shot (on the left is the rectangular image and on the right is
>>>> the
>>>> cropped square image, low pass filtered to 20A) that shows what we
>>>> see.
>>>> Thanks!
>>>>
>>>>
>>>> Weiwei
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* Shawn Zheng <[log in to unmask]>
>>>> *Sent:* Thursday, October 13, 2016 1:35 PM
>>>> *To:* Weiwei Wang
>>>> *Cc:* [log in to unmask]
>>>> *Subject:* Re: [ccpem] MotionCor2
>>>>
>>>> Hi Weiwei and Tat,
>>>>
>>>> I assume the vertical lines are seen in the Fourier transform,
>>>> correct?
>>>> If this is the case, combined with Tat's workaround, I would think
>>>> these
>>>> lines are due to orientation mismatch between frames and gain
>>>> reference.
>>>> The new version of MotionCor2 allows to rotate and flip gain reference
>>>> before it is applied to frames. These options can be enabled by
>>>> "-FlipGain"
>>>> and "-RotGain". You can download from http://msg.ucsf.edu/em/so
>>>> ftware/index.html.
>>>>
>>>> Best
>>>> Shawn
>>>>
>>>> On Thu, Oct 13, 2016 at 9:38 AM, Weiwei Wang <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> Hi Shawn,
>>>>>
>>>>>
>>>>> Thank you for making this great software!
>>>>>
>>>>>
>>>>> We are currently trying to use it for motion correction. There is one
>>>>> problem that we encountered.
>>>>>
>>>>>
>>>>> The dimension of our K2 sensor (super-resolution mode) is 7420 x
>>>>> 7676.
>>>>> If we use this original size, the dose filtered output (*DW.mrc, with
>>>>> 5x5
>>>>> patches) looks dim and has vertical lines (along the long dimension).
>>>>> However cropping the image into 7420 x 7420 using the -Crop option
>>>>> solves the problem.
>>>>>
>>>>>
>>>>> I wonder if square images are required? Thanks a lot!
>>>>>
>>>>>
>>>>> Best,
>>>>>
>>>>> Weiwei
>>>>> ------------------------------
>>>>> *From:* Collaborative Computational Project in Electron
>>>>> cryo-Microscopy <[log in to unmask]> on behalf of Shawn Zheng <
>>>>> [log in to unmask]>
>>>>> *Sent:* Thursday, October 13, 2016 11:23 AM
>>>>> *To:* [log in to unmask]
>>>>> *Subject:* [ccpem] MotionCor2
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I am the author of MotionCor2. I will be happy to answer MotionCor2
>>>>> questions and take your suggestions,
>>>>>
>>>>> Best,
>>>>>
>>>>> Shawn
>>>>>
>>>>
>>>>
>>>
>>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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