[3dem] fc4i defect
Ji-Joon Song
songj at kaist.ac.kr
Wed Jan 24 00:24:26 PST 2024
Hi Daniel,
Yes, we tried all possible combinations for the gain rotation/flipping.
Thanks,
Ji-Joon
===============
Ji-Joon Song, Ph.D.
Professor
Dep. Biological Sciences
KAIST, Korea
songj at kaist.ac.kr mailto:songj at kaist.ac.kr
jijoonsong.kaist at gmail.com mailto:jijoonsong.kaist at gmail.com
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===============
-----Original Message-----From: "Daniel Asarnow" <asarnow at msg.ucsf.edu>To: "Ji-Joon Song" <songj at kaist.ac.kr>; Cc: "Jin Young Kang" <jykang59 at kaist.ac.kr>; "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>; "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>; "김나윤" <nayunkim at kaist.ac.kr>; Sent: 2024-01-24 (We) 17:21:26 (UTC+09:00)Subject: Re: [3dem] fc4i defectHi 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 mailto: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 mailto:songj at kaist.ac.kr
jijoonsong.kaist at gmail.com mailto:jijoonsong.kaist at gmail.com
https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$ https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$
Song-KAIST ZOOM link:
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===============
-----Original Message-----
From: "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp mailto:tnakane.protein at osaka-u.ac.jp>
To: "Ji-Joon Song" <songj at kaist.ac.kr mailto:songj at kaist.ac.kr>; "Jin Young Kang" <jykang59 at kaist.ac.kr mailto:jykang59 at kaist.ac.kr>;
Cc: "3dem at ncmir.ucsd.edu mailto:3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu mailto: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 mailto:songj at kaist.ac.kr
>
> jijoonsong.kaist at gmail.com mailto:jijoonsong.kaist at gmail.com
>
>
>
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$ 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$ 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 mailto:tnakane.protein at osaka-u.ac.jp>
> To: "Jin Young Kang" <jykang59 at kaist.ac.kr mailto:jykang59 at kaist.ac.kr>; "Ji-Joon Song" <songj at kaist.ac.kr mailto:songj at kaist.ac.kr>;
> Cc: "3dem at ncmir.ucsd.edu mailto:3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu mailto: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 mailto:songj at kaist.ac.kr>
>> To: "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp mailto:tnakane.protein at osaka-u.ac.jp>;
>> Cc: "3dem at ncmir.ucsd.edu mailto:3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu mailto: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 mailto:songj at kaist.ac.kr
>>
>> jijoonsong.kaist at gmail.com mailto:jijoonsong.kaist at gmail.com
>>
>>
>>
>> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$ 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$ 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 mailto:tnakane.protein at osaka-u.ac.jp>
>> To: "Ji-Joon Song" <songj at kaist.ac.kr mailto:songj at kaist.ac.kr>;
>> Cc: "3dem at ncmir.ucsd.edu mailto:3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu mailto: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 mailto:songj at kaist.ac.kr
>>>
>>> jijoonsong.kaist at gmail.com mailto:jijoonsong.kaist at gmail.com
>>>
>>>
>>>
>>> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$ 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$ 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 mailto:tnakane.protein at osaka-u.ac.jp" <tnakane.protein at osaka-u.ac.jp mailto:tnakane.protein at osaka-u.ac.jp>
>>> To: "Ji-Joon Song" <songj at kaist.ac.kr mailto:songj at kaist.ac.kr>; "3dem at ncmir.ucsd.edu mailto:3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu mailto: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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