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<p>Dear Ji-Joon & Jin Young,</p>
<p>On our Falcon4i, we have 3 defect pixel lines and we are
succesfully using it for both single-particle and cryo-ET.</p>
<p>However, we noticed that it is important that the dose-rate at
which the gain reference is acquired should roughly match the
dose-rate used during data-collection. Luckily, there is still
quite some variability in dose-rate where the gain reference works
well.</p>
<p>Hope that helps,</p>
<p>Maarten <br>
</p>
<pre class="moz-signature"
signature-switch-id="879a8b6b-a1bc-4e91-98bb-b4497cdbd5b4" cols="72">Maarten Tuijtel PhD
Postdoctoral Researcher
Department of Molecular Sociology
Room B1.105
Max Planck Institute of Biophysics
Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
Office phone number: +4969 6303 3508</pre>
<div class="moz-cite-prefix">On 24/01/2024 09:24, Ji-Joon Song
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:sa77j1n4vktt.sa77j1n50l2z.g3@dooray.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div style="font-family: system-ui; font-size: 14px">
<div>Hi Daniel, </div>
<div>Yes, we tried all possible combinations for the gain
rotation/flipping.</div>
<div>Thanks, </div>
<div><br>
</div>
<div>Ji-Joon</div>
<div><br>
</div>
<div><br>
</div>
<!-- begin signature -->
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<p
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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>
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style="font-family: Arial, sans-serif;"><a
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moz-do-not-send="true"><span
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<p
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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!HP8139lff2TJGZJq7Ns-pNBgfsO6dTL3RA2tipJ_rfNDlS5FAqd909CCC3CMk1G-kxtlZ-lC3UYFkFl8oa8$"
moz-do-not-send="true">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>
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<br>
<br>
-----Original Message-----<br>
From: "Daniel Asarnow" <a class="moz-txt-link-rfc2396E" href="mailto:asarnow@msg.ucsf.edu"><asarnow@msg.ucsf.edu></a><br>
To: "Ji-Joon Song" <a class="moz-txt-link-rfc2396E" href="mailto:songj@kaist.ac.kr"><songj@kaist.ac.kr></a>; <br>
Cc: "Jin Young Kang" <a class="moz-txt-link-rfc2396E" href="mailto:jykang59@kaist.ac.kr"><jykang59@kaist.ac.kr></a>; "Takanori
Nakane" <a class="moz-txt-link-rfc2396E" href="mailto:tnakane.protein@osaka-u.ac.jp"><tnakane.protein@osaka-u.ac.jp></a>;
<a class="moz-txt-link-rfc2396E" href="mailto:3dem@ncmir.ucsd.edu">"3dem@ncmir.ucsd.edu"</a> <a class="moz-txt-link-rfc2396E" href="mailto:3dem@ncmir.ucsd.edu"><3dem@ncmir.ucsd.edu></a>; "김나윤"
<a class="moz-txt-link-rfc2396E" href="mailto:nayunkim@kaist.ac.kr"><nayunkim@kaist.ac.kr></a>; <br>
Sent: 2024-01-24 (We) 17:21:26 (UTC+09:00)<br>
Subject: Re: [3dem] fc4i defect<br>
<br>
<div dir="ltr">
<div>Hi Ji-Joon,</div>
<div>Just wanted to ask - have you tried all possible values for
the gain rotation / flipping?</div>
<div><br>
</div>
<div>Best,</div>
<div>-da<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Jan 24, 2024 at 12:08 AM Ji-Joon Song
<<a href="mailto:songj@kaist.ac.kr" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a>>
wrote:<br>
</div>
<blockquote
style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex;">!-------------------------------------------------------------------|<br>
This Message Is From an External Sender<br>
This message came from outside your organization.<br>
|-------------------------------------------------------------------!<br>
<br>
You meant actual gainreference.mrc.<br>
I will try what you suggest and will get you back shorlty.<br>
Many thanks, <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"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a><br>
<br>
<a href="mailto:jijoonsong.kaist@gmail.com" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">jijoonsong.kaist@gmail.com</a><br>
<br>
<br>
<br>
<a
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<br>
<br>
<br>
<br>
<br>
Song-KAIST ZOOM link:<br>
<br>
<a
href="https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYVka3Gs0$"
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<br>
<br>
===============<br>
<br>
<br>
<br>
<br>
-----Original Message-----<br>
From: "Takanori Nakane" <<a
href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">tnakane.protein@osaka-u.ac.jp</a>><br>
To: "Ji-Joon Song" <<a href="mailto:songj@kaist.ac.kr"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">songj@kaist.ac.kr</a>>;
"Jin Young Kang" <<a href="mailto:jykang59@kaist.ac.kr"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jykang59@kaist.ac.kr</a>>;
<br>
Cc: "<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>"
<<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>>;
<br>
Sent: 2024-01-24 (We) 16:57:06 (UTC+09:00)<br>
Subject: Re: [3dem] fc4i defect<br>
<br>
Hi,<br>
<br>
> Even if we put defect file having two columns as
defects, supposing <br>
that this will mask the two defect lines, this does not always
work. The <br>
lines sometime continue to appear depending on data sets.<br>
<br>
"defect file": do you mean a text file that can be specified
apart from<br>
a gain reference?<br>
<br>
Did you inspect the gain reference and modify it as I
suggested?<br>
If not, please do so.<br>
<br>
I cannot comment on CryoET as I don't do it at all.<br>
<br>
> Is this a kind of a bad detector that TFS definitely
should replace?<br>
<br>
It is almost impossible (economically) to make a perfect,
defect free<br>
detector. Each manufacturer defines a maximum limit of defects
for<br>
an "acceptable" chip.<br>
<br>
"The TF manufacturer claims that the detector is within their
spec."<br>
suggests that these two lines are within their spec and they
are not<br>
willing to replace it, unfortunately.<br>
<br>
The situation is the same as hot and dead pixels on an LCD
monitor.<br>
<br>
From a developer's perspective, I hope detector software to
fill<br>
defective pixels. Different detectors have different defect
patterns.<br>
For example, Gatan's K2 detectors tend to have strange 3x3
blobs<br>
(as mentioned in the MotionCor2 paper) but rarely have<br>
line defects. I don't want to implement detector specific
correction<br>
algorithms in RELION. This should be handled by the detector
software.<br>
<br>
Best regards,<br>
<br>
Takanori Nakane<br>
<br>
On 2024/01/24 16:43, Ji-Joon Song wrote:<br>
> Hi Takanori,<br>
> <br>
> it is not straightforward.<br>
> 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.<br>
> In addition, as Jin Young raised an issue, we are more
concerned about cryo-ET.<br>
> Is this a kind of a bad detector that TFS definitely
should replace?<br>
> Many thanks,<br>
> <br>
> Ji-Joon<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"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a><br>
> <br>
> <a href="mailto:jijoonsong.kaist@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jijoonsong.kaist@gmail.com</a><br>
> <br>
> <br>
> <br>
> <a
href="https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$"
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<br>
> <br>
> <br>
> <br>
> <br>
> Song-KAIST ZOOM link:<br>
> <br>
> <a
href="https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYVka3Gs0$"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYVka3Gs0$</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"
moz-do-not-send="true" class="moz-txt-link-freetext">tnakane.protein@osaka-u.ac.jp</a>><br>
> To: "Jin Young Kang" <<a
href="mailto:jykang59@kaist.ac.kr" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">jykang59@kaist.ac.kr</a>>;
"Ji-Joon Song" <<a href="mailto:songj@kaist.ac.kr"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">songj@kaist.ac.kr</a>>;<br>
> Cc: "<a href="mailto:3dem@ncmir.ucsd.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>" <<a
href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>>;<br>
> Sent: 2024-01-24 (We) 16:15:39 (UTC+09:00)<br>
> Subject: Re: [3dem] fc4i defect<br>
> <br>
> Hi,<br>
> <br>
> Did you check the gain values on the white line and the
gray line?<br>
> Is white 0? If so, making the gray line 0 will also mask
it,<br>
> at least on RELION. I don't know how other programs
handle defects.<br>
> <br>
> Best regards,<br>
> <br>
> Takanori Nakane<br>
> <br>
> On 2024/01/24 16:08, Jin Young Kang wrote:<br>
>> 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"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a>><br>
>> To: "Takanori Nakane" <<a
href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">tnakane.protein@osaka-u.ac.jp</a>>;<br>
>> Cc: "<a href="mailto:3dem@ncmir.ucsd.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>" <<a
href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">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"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a><br>
>><br>
>> <a href="mailto:jijoonsong.kaist@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">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$"
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>><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$"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$</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"
moz-do-not-send="true" class="moz-txt-link-freetext">tnakane.protein@osaka-u.ac.jp</a>><br>
>> To: "Ji-Joon Song" <<a
href="mailto:songj@kaist.ac.kr" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a>>;<br>
>> Cc: "<a href="mailto:3dem@ncmir.ucsd.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>" <<a
href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">songj@kaist.ac.kr</a><br>
>>><br>
>>> <a href="mailto:jijoonsong.kaist@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">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$"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$</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$"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$</a><br>
>>><br>
>>> ===============<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> -----Original Message-----<br>
>>> From: "<a
href="mailto:tnakane.protein@osaka-u.ac.jp" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">tnakane.protein@osaka-u.ac.jp</a>"
<<a href="mailto:tnakane.protein@osaka-u.ac.jp"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">tnakane.protein@osaka-u.ac.jp</a>><br>
>>> To: "Ji-Joon Song" <<a
href="mailto:songj@kaist.ac.kr" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">songj@kaist.ac.kr</a>>;
"<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a>"
<<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">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>
>> 3dem mailing list<br>
>> <a href="mailto:3dem@ncmir.ucsd.edu" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">3dem@ncmir.ucsd.edu</a><br>
>> <a
href="https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!LQC6Cpwp!vfAjoISjj7Dr5HXPK8OYk4fhCcmgdHIwnqv7chy_RbdCdxWl4BnpOr0_Y8ljkKAVWsoZ_ucWTrQDnCR9egA$"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!LQC6Cpwp!vfAjoISjj7Dr5HXPK8OYk4fhCcmgdHIwnqv7chy_RbdCdxWl4BnpOr0_Y8ljkKAVWsoZ_ucWTrQDnCR9egA$</a>
<br>
_______________________________________________<br>
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<a
href="https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!LQC6Cpwp!vfAjoISjj7Dr5HXPK8OYk4fhCcmgdHIwnqv7chy_RbdCdxWl4BnpOr0_Y8ljkKAVWsoZ_ucWTrQDnCR9egA$"
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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