[3dem] fc4i defect

Wed Jan 24 00:21:10 PST 2024

Hi Ji-Joon,
Just wanted to ask - have you tried all possible values for the gain
rotation / flipping?

Best,
-da

On Wed, Jan 24, 2024 at 12:08 AM Ji-Joon Song <songj at kaist.ac.kr> wrote:

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> You meant actual gainreference.mrc.
> I will try what you suggest and will get you back shorlty.
> Many thanks,
>
> JI-Joon
>
>
>
>
> ===============
>
> Ji-Joon Song, Ph.D.
>
>
> Professor
>
> Dep. Biological Sciences
>
> KAIST, Korea
>
> songj at kaist.ac.kr
>
> jijoonsong.kaist at gmail.com
>
>
>
>
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>
>
>
> Song-KAIST ZOOM link:
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> ===============
>
>
>
>
> -----Original Message-----
> From:  "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>
> To:     "Ji-Joon Song" <songj at kaist.ac.kr>;  "Jin Young Kang" <
> jykang59 at kaist.ac.kr>;
> Cc:     "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> Sent:  2024-01-24 (We) 16:57:06 (UTC+09:00)
> Subject: Re: [3dem] fc4i defect
>
> Hi,
>
>  > Even if we put defect file having two columns as defects, supposing
> that this will mask the two defect lines, this does not always work. The
> lines sometime continue to appear depending on data sets.
>
> "defect file": do you mean a text file that can be specified apart from
> a gain reference?
>
> Did you inspect the gain reference and modify it as I suggested?
> If not, please do so.
>
> I cannot comment on CryoET as I don't do it at all.
>
>  > Is this a kind of a bad detector that TFS definitely should replace?
>
> It is almost impossible (economically) to make a perfect, defect free
> detector. Each manufacturer defines a maximum limit of defects for
> an "acceptable" chip.
>
> "The TF manufacturer claims that the detector is within their spec."
> suggests that these two lines are within their spec and they are not
> willing to replace it, unfortunately.
>
> The situation is the same as hot and dead pixels on an LCD monitor.
>
>  From a developer's perspective, I hope detector software to fill
> defective pixels. Different detectors have different defect patterns.
> For example, Gatan's K2 detectors tend to have strange 3x3 blobs
> (as mentioned in the MotionCor2 paper) but rarely have
> line defects. I don't want to implement detector specific correction
> algorithms in RELION. This should be handled by the detector software.
>
> Best regards,
>
> Takanori Nakane
>
> On 2024/01/24 16:43, Ji-Joon Song wrote:
> > Hi Takanori,
> >
> > it is not straightforward.
> > Even if we put defect file having two columns as defects, supposing that
> this will mask the two defect lines, this does not always work. The lines
> sometime continue to appear depending on data sets.
> > In addition, as Jin Young raised an issue, we are more concerned about
> cryo-ET.
> > Is this a kind of a bad detector that TFS definitely should replace?
> > Many thanks,
> >
> > Ji-Joon
> >
> >
> >
> > ===============
> >
> > Ji-Joon Song, Ph.D.
> >
> >
> > Professor
> >
> > Dep. Biological Sciences
> >
> > KAIST, Korea
> >
> > songj at kaist.ac.kr
> >
> > jijoonsong.kaist at gmail.com
> >
> >
> >
> >
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$
> >
> >
> >
> >
> > Song-KAIST ZOOM link:
> >
> >
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYVka3Gs0$
> >
> > ===============
> >
> >
> >
> >
> > -----Original Message-----
> > From:  "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>
> > To:     "Jin Young Kang" <jykang59 at kaist.ac.kr>;  "Ji-Joon Song" <
> songj at kaist.ac.kr>;
> > Cc:     "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> > Sent:  2024-01-24 (We) 16:15:39 (UTC+09:00)
> > Subject: Re: [3dem] fc4i defect
> >
> > Hi,
> >
> > Did you check the gain values on the white line and the gray line?
> > Is white 0? If so, making the gray line 0 will also mask it,
> > at least on RELION. I don't know how other programs handle defects.
> >
> > Best regards,
> >
> > Takanori Nakane
> >
> > On 2024/01/24 16:08, Jin Young Kang wrote:
> >> Hi Takanori and 3dem community,
> >>
> >>
> >> I hope everyone is well. I wanted to join the discussion Ji-Joon raised
> in our 3dem community. I thank Ji-Joon for raising this important topic.
> >> I'm part of the same institute as Ji-Joon, and I share his concerns
> about the potential impact of a certain defect, particularly in the context
> of cryo-ET.
> >>
> >> Our data analysis has revealed some peculiar 2D classes with particles
> clustering along the defect line. Unfortunately, due to the defect's
> central location on the display, we anticipate a significant loss of
> particles. However, for single particle analysis, we do have the option to
> exclude these unusual particle images (I attached a figure showing this).
> >>
> >> However, how about cryo-ET? Given that the defect is situated in the
> central area, avoiding it during data collection is not feasible. This is
> especially concerning as, during cryo-ET, we need to capture tilt series,
> where objects undergo substantial movement with varying tilt angles. This
> raises questions about the quality of the data we can obtain.
> >>
> >> Our resource center staff have invested a significant amount of effort
> in establishing a state-of-the-art 300keV cryo-EM facility on campus, and
> we are determined to make the most of this valuable resource. Therefore, we
> are eager to find a solution that ensures we can collect the highest
> quality cryo-ET data without the interference of defects.
> >>
> >> I would appreciate your valuable insights and advice on how we can
> effectively address this issue. Your expertise and perspectives would be
> greatly appreciated in helping us optimize the use of our cryo-EM facility
> and advance our research goals. (Of course, if possible, we would like to
> request a new camera chip...)
> >>
> >> Thank you in advance for your contributions to this discussion, and I
> look forward to hearing your thoughts on this matter.
> >>
> >> Best regards,
> >> Jin Young
> >>
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From:  "Ji-Joon Song" <songj at kaist.ac.kr>
> >> To:     "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>;
> >> Cc:     "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> >> Sent:  2024-01-24 (We) 13:39:56 (UTC+09:00)
> >> Subject: Re: [3dem] fc4i defect
> >>
> >> Thanks!
> >> We will look into it more.
> >> Best,
> >>
> >> JI-Joon
> >>
> >>
> >>
> >>
> >> ===============
> >>
> >> Ji-Joon Song, Ph.D.
> >>
> >>
> >> Professor
> >>
> >> Dep. Biological Sciences
> >>
> >> KAIST, Korea
> >>
> >> songj at kaist.ac.kr
> >>
> >> jijoonsong.kaist at gmail.com
> >>
> >>
> >>
> >>
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$
> >>
> >>
> >>
> >>
> >> Song-KAIST ZOOM link:
> >>
> >>
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$
> >>
> >> ===============
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From:  "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>
> >> To:     "Ji-Joon Song" <songj at kaist.ac.kr>;
> >> Cc:     "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> >> Sent:  2024-01-24 (We) 13:35:53 (UTC+09:00)
> >> Subject: Re: [3dem] fc4i defect
> >>
> >> Hi,
> >>
> >>    > can you inform me how I can set defective lines to have 0s in the
> >> gain reference?
> >>
> >> If the camera software is aware of the defect lines,
> >> the values in the gain reference should be zero.
> >> But different versions of the camera software may behave differently.
> >> Please ask your TFS support staff.
> >>
> >> Alternatively, you can read the gain reference (.gain is a TIFF file),
> >> set 0, and write it back by a simple Python script.
> >>
> >> Best regards,
> >>
> >> Takanori Nakane
> >>
> >> On 2024/01/24 13:31, Ji-Joon Song wrote:
> >>>
> >>> Hi Takanori,
> >>>
> >>> Thank you for the info.
> >>> Do you mean to set 0s to the defected pixels (lines) at a defect file?
> >>> or can you inform me how I  can set defective lines to have 0s in the
> gain reference?
> >>> Thanks in advance.
> >>>
> >>> Ji-Joon
> >>>
> >>>
> >>>
> >>>
> >>> ===============
> >>>
> >>> Ji-Joon Song, Ph.D.
> >>>
> >>>
> >>> Professor
> >>>
> >>> Dep. Biological Sciences
> >>>
> >>> KAIST, Korea
> >>>
> >>> songj at kaist.ac.kr
> >>>
> >>> jijoonsong.kaist at gmail.com
> >>>
> >>>
> >>>
> >>>
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$
> >>>
> >>>
> >>>
> >>>
> >>> Song-KAIST ZOOM link:
> >>>
> >>>
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$
> >>>
> >>> ===============
> >>>
> >>>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From:  "tnakane.protein at osaka-u.ac.jp" <tnakane.protein at osaka-u.ac.jp>
> >>> To:     "Ji-Joon Song" <songj at kaist.ac.kr>;  "3dem at ncmir.ucsd.edu" <
> 3dem at ncmir.ucsd.edu>;
> >>> Cc:
> >>> Sent:  2024-01-24 (We) 10:30:09 (UTC+09:00)
> >>> Subject: Re: [3dem] fc4i defect
> >>>
> >>> Hi,
> >>>
> >>>> Our institute recently installed a brand new Titan krios with Facon4i.
> >>>> But, we are having an issue in the detector as there are two
> consecutive lines of defect in the detector.
> >>>> When we acquire and motioncorr micrographs, we have a thick black
> line as attached.
> >>>> This line sometimes disappears when we use specific programs such as
> CryoSparc but not working Relion.
> >>>> The TF manufacturer claims that the detector is within their spec.
> >>>> I would like to request any advice regarding this issue.
> >>>
> >>> Please make sure pixels on these defective lines have 0s in the gain
> reference.
> >>> RELION tries to conceal defects by randomly picking values from a good
> pixel nearby.
> >>>
> >>> That being said, information on defective pixels is lost and cannot be
> recovered.
> >>> Defect correction only conceals, not fixes, the problem.
> >>> In my experience, one can throw away all particles on a defective line
> and the resolution does not change much.
> >>>
> >>> Best regards,
> >>>
> >>> Takanori Nakane
> >> _______________________________________________
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> >> 3dem at ncmir.ucsd.edu
> >>
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