[3dem] fc4i defect

[Eugene Pichkur]

The only correct solution is to force the manufacturer to replace the
sensor with a new one.
High-tech equipment worth hundreds of thousands $$ should not have such
defects (if this is actually a sensor defect, not a software bug).


On Wed, Jan 24, 2024 at 10:11 AM Jin Young Kang <jykang59 at kaist.ac.kr>
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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