<div style="font-family: system-ui; font-size: 14px"><div><br></div><div>Hi Jonny,</div><div><br></div><div>Thank you for the comments.</div><div>I talked with Marin and he kindly offered the camera correction program.</div><div>All my best, </div><div><br></div><div>Ji-Joon</div><div><br></div><!-- begin signature --><div style="color: rgb(0, 0, 0); font-family: -webkit-standard; font-style: normal; font-weight: normal; text-align: start; text-indent: 0px; text-decoration: none;"><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;">===============</span></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;">Ji-Joon Song, Ph.D.</span></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><span style="font-family: Arial, sans-serif;"><br><strong>Professor</strong></span></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;">Dep. Biological Sciences</span></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;">KAIST, Korea</span></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;"><a href="mailto:songj@kaist.ac.kr">songj@kaist.ac.kr</a></span></strong></p><div style="line-height: 1;"><a href="mailto:jijoonsong.kaist@gmail.com" rel="noopener noreferrer" target="_blank"><span style="font-family: Arial, Helvetica, sans-serif; font-size: 11pt;"><strong>jijoonsong.kaist@gmail.com</strong></span></a></div><div style="line-height: 1;"><br></div><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;"><a href="https://urldefense.com/v3/__http://www.song-kaist.org/__;!!Mih3wA!FXfWl3Yb9jty5qYbDFMHY9dattQoik8UdG3PUiTPm2D9cXBqfZILa7MRdNQr9xAWl4SHKhAToXD_URtJzQE$">www.song-kaist.org</a></span></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><br></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;">Song-KAIST ZOOM link:</span></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><a href="https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!FXfWl3Yb9jty5qYbDFMHY9dattQoik8UdG3PUiTPm2D9cXBqfZILa7MRdNQr9xAWl4SHKhAToXD_10dwZKE$">https://kaist.zoom.us/j/89910489123</a></strong></p><p style="margin: 0in; font-size: 15px; font-family: Calibri, sans-serif; color: rgb(0, 0, 0); line-height: 1;"><strong><span style="font-family: Arial, sans-serif;">===============</span></strong></p></div><div style="color: rgb(0, 0, 0);font-family: -webkit-standard;font-style: normal;font-weight: normal;text-align: start;text-indent: 0px;text-decoration: none;">H</div><!-- end signature --></div><br><br>-----Original Message-----<br>From: "Jonathan Flores" <florejo@ohsu.edu><br>To: "Marin van Heel" <marin.vanheel@googlemail.com>; "Jin Young Kang" <jykang59@kaist.ac.kr>; "ccpem@jiscmail.ac.uk" <ccpem@jiscmail.ac.uk>; <br>Cc: "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu>; "Ji-Joon Song" <songj@kaist.ac.kr>; <br>Sent: 2024-01-30 (Tu) 05:30:53 (UTC+09:00)<br>Subject: Re: Re: [3dem] fc4i defect<br><br><div class="dooray_mail_4830370475972217591">
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<p><span lang="EN-US" style="font-size:11.0pt; mso-fareast-language:EN-US;">Not sure if it helps your issue but…: I’ve used pretty much the IMAGIC-based approach referenced from Marin & Sayan to remove scale bars from NSEM images. Works great!<xo:p></xo:p></span></p>
<p><span lang="EN-US" style="font-size:11.0pt; mso-fareast-language:EN-US;"><xo:p> </xo:p></span></p>
<p><span lang="EN-US" style="font-size:11.0pt; mso-fareast-language:EN-US;">Good luck,<xo:p></xo:p></span></p>
<p><span lang="EN-US" style="font-size:11.0pt; mso-fareast-language:EN-US;">Jonny <xo:p></xo:p></span></p>
<p><span style="font-size:11.0pt; mso-fareast-language:EN-US;"><xo:p> </xo:p></span></p>
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<p style="margin-bottom:12.0pt;"><b><span style="font-size:12.0pt; font-family:Aptos,sans-serif; color:black;">From:
</span></b><span style="font-size:12.0pt; font-family:Aptos,sans-serif; color:black;">3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Marin van Heel <marin.vanheel@googlemail.com><br>
<b>Date: </b>Wednesday, 24 January 2024 at 20.43<br>
<b>To: </b>Jin Young Kang <jykang59@kaist.ac.kr>, ccpem@jiscmail.ac.uk <ccpem@jiscmail.ac.uk><br>
<b>Cc: </b>3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu>, Ji-Joon Song <songj@kaist.ac.kr><br>
<b>Subject: </b>[EXTERNAL] Re: [3dem] fc4i defect<xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;">Dear All<xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;"><xo:p> </xo:p></span></p>
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<div>
<p><span style="font-size:11.0pt;">This discussion is about camera correction! It is an excellent example of what goes wrong when the camera correction is not performed as it should be.<xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;">The very strong residual line is not sufficiently removed and thus becomes a dominant feature that causes misalignments!<xo:p></xo:p></span></p>
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<div>
<p><span style="font-size:11.0pt;">We published an extensive story about how to do it correctly:
<i>A posteriori</i> correction of camera characteristics from large image data sets
<xo:p></xo:p></span></p>
</div>
<div>
<p><span style="font-size:11.0pt;">A free download! <a href="https://urldefense.com/v3/__https:/www.nature.com/articles/srep10317__;!!Mih3wA!C3bS10PG03zyLhYhXhrKTB0CcoLJNSOqRriiA6Iu9Cbmzxe60LhluyMp6KZ2MrH-MAQ_ynhNrHuYr1LbkU10WYPA2MR8Sg$" target="_blank">
https://www.nature.com/articles/srep10317</a><xo:p></xo:p></span></p>
</div>
<div>
<p><span style="font-size:11.0pt;">It is a standard procedure in the IMAGIC software system. There is also a specific Camera correction GUI being prepared by Image Science GmbH Berlin<xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;"><xo:p> </xo:p></span></p>
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<p><span style="font-size:11.0pt;">Cheers,<xo:p></xo:p></span></p>
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<div>
<p><span style="font-size:11.0pt;">Marin and Sayan<xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;"><xo:p> </xo:p></span></p>
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<p style="margin-bottom:12.0pt;"><span style="font-size:11.0pt;"><img border="0" width="578" height="550" style="width:6.0208in; height:5.7291in;" id="_x0000_i1025" src="cid:3726753703238139936.3726755142668923579@dooray.com"><xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;"><xo:p> </xo:p></span></p>
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<p><span style="font-size:11.0pt;"><xo:p> </xo:p></span></p>
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<p><span style="font-size:11.0pt;">On Wed, Jan 24, 2024 at 4:11 AM Jin Young Kang <<a href="mailto:jykang59@kaist.ac.kr" target="_blank">jykang59@kaist.ac.kr</a>> wrote:<xo:p></xo:p></span></p>
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<p><span style="font-size:11.0pt;">Hi Takanori and 3dem community,
<br>
<br>
<br>
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.<br>
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.<br>
<br>
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).<br>
<br>
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.<br>
<br>
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.<br>
<br>
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...) <br>
<br>
Thank you in advance for your contributions to this discussion, and I look forward to hearing your thoughts on this matter.<br>
<br>
Best regards,<br>
Jin Young<br>
<br>
<br>
<br>
<br>
<br>
-----Original Message-----<br>
From: "Ji-Joon Song" <<a href="mailto:songj@kaist.ac.kr" target="_blank">songj@kaist.ac.kr</a>><br>
To: "Takanori Nakane" <<a href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank">tnakane.protein@osaka-u.ac.jp</a>>;
<br>
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>>;
<br>
Sent: 2024-01-24 (We) 13:39:56 (UTC+09:00)<br>
Subject: Re: [3dem] fc4i defect<br>
<br>
Thanks!<br>
We will look into it more.<br>
Best, <br>
<br>
JI-Joon<br>
<br>
<br>
<br>
<br>
===============<br>
<br>
Ji-Joon Song, Ph.D.<br>
<br>
<br>
Professor<br>
<br>
Dep. Biological Sciences<br>
<br>
KAIST, Korea<br>
<br>
<a href="mailto:songj@kaist.ac.kr" target="_blank">songj@kaist.ac.kr</a><br>
<br>
<a href="mailto:jijoonsong.kaist@gmail.com" target="_blank">jijoonsong.kaist@gmail.com</a><br>
<br>
<br>
<br>
<a href="https://urldefense.com/v3/__http:/www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$" target="_blank">https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$</a>
<br>
<br>
<br>
<br>
<br>
Song-KAIST ZOOM link:<br>
<br>
<a href="https://urldefense.com/v3/__https:/kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$" target="_blank">https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$</a>
<br>
<br>
===============<br>
<br>
<br>
<br>
<br>
-----Original Message-----<br>
From: "Takanori Nakane" <<a href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank">tnakane.protein@osaka-u.ac.jp</a>><br>
To: "Ji-Joon Song" <<a href="mailto:songj@kaist.ac.kr" target="_blank">songj@kaist.ac.kr</a>>;
<br>
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>>;
<br>
Sent: 2024-01-24 (We) 13:35:53 (UTC+09:00)<br>
Subject: Re: [3dem] fc4i defect<br>
<br>
Hi,<br>
<br>
> can you inform me how I can set defective lines to have 0s in the <br>
gain reference?<br>
<br>
If the camera software is aware of the defect lines,<br>
the values in the gain reference should be zero.<br>
But different versions of the camera software may behave differently.<br>
Please ask your TFS support staff.<br>
<br>
Alternatively, you can read the gain reference (.gain is a TIFF file),<br>
set 0, and write it back by a simple Python script.<br>
<br>
Best regards,<br>
<br>
Takanori Nakane<br>
<br>
On 2024/01/24 13:31, Ji-Joon Song wrote:<br>
> <br>
> Hi Takanori,<br>
> <br>
> Thank you for the info.<br>
> Do you mean to set 0s to the defected pixels (lines) at a defect file?<br>
> or can you inform me how I can set defective lines to have 0s in the gain reference?<br>
> Thanks in advance.<br>
> <br>
> Ji-Joon<br>
> <br>
> <br>
> <br>
> <br>
> ===============<br>
> <br>
> Ji-Joon Song, Ph.D.<br>
> <br>
> <br>
> Professor<br>
> <br>
> Dep. Biological Sciences<br>
> <br>
> KAIST, Korea<br>
> <br>
> <a href="mailto:songj@kaist.ac.kr" target="_blank">songj@kaist.ac.kr</a><br>
> <br>
> <a href="mailto:jijoonsong.kaist@gmail.com" target="_blank">jijoonsong.kaist@gmail.com</a><br>
> <br>
> <br>
> <br>
> <a href="https://urldefense.com/v3/__http:/www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$" target="_blank">
https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$</a>
<br>
> <br>
> <br>
> <br>
> <br>
> Song-KAIST ZOOM link:<br>
> <br>
> <a href="https://urldefense.com/v3/__https:/kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$" target="_blank">
https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$</a>
<br>
> <br>
> ===============<br>
> <br>
> <br>
> <br>
> <br>
> -----Original Message-----<br>
> From: "<a href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank">tnakane.protein@osaka-u.ac.jp</a>" <<a href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank">tnakane.protein@osaka-u.ac.jp</a>><br>
> To: "Ji-Joon Song" <<a href="mailto:songj@kaist.ac.kr" target="_blank">songj@kaist.ac.kr</a>>; "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>>;<br>
> Cc:<br>
> Sent: 2024-01-24 (We) 10:30:09 (UTC+09:00)<br>
> Subject: Re: [3dem] fc4i defect<br>
> <br>
> Hi,<br>
> <br>
>> Our institute recently installed a brand new Titan krios with Facon4i.<br>
>> But, we are having an issue in the detector as there are two consecutive lines of defect in the detector.<br>
>> When we acquire and motioncorr micrographs, we have a thick black line as attached.<br>
>> This line sometimes disappears when we use specific programs such as CryoSparc but not working Relion.<br>
>> The TF manufacturer claims that the detector is within their spec.<br>
>> I would like to request any advice regarding this issue.<br>
> <br>
> Please make sure pixels on these defective lines have 0s in the gain reference.<br>
> RELION tries to conceal defects by randomly picking values from a good pixel nearby.<br>
> <br>
> That being said, information on defective pixels is lost and cannot be recovered.<br>
> Defect correction only conceals, not fixes, the problem.<br>
> In my experience, one can throw away all particles on a defective line and the resolution does not change much.<br>
> <br>
> Best regards,<br>
> <br>
> Takanori Nakane<br>
_______________________________________________<br>
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