[3dem] fc4i defect

[Ji-Joon Song]

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



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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>; 
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