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Dear Oliver<br>
<br>
Unfortunately, that is not feasible in general. Our claim is that
using the "<i>a posteriori</i> camera correction" you will end up
with a better/larger set of particles simply because there is less
"fixed pattern noise" in the data (and also less fixed pattern
gain noise.) In other words the "with" versus the "without"
picking coordinates would be different, the number of picked
particles should be larger, the number of rejected particles
further down the pipeline should be smaller, and the
rotation/shift/ movie alignment parameters different. If one
would apply "camera-corrected picking coordinates" to not
corrected images, one would improve the "not corrected" results
beyond the "fully not-corrected" processing results. These would
still be a bit worse than the original fully-corrected processing
results. If, on the other hand, one would apply the "not
corrected" co-ordinates to the "corrected" images, those would do
slightly better than the <br>
"fully not-corrected" processing results due to the removal of the
fixed pattern noise. However, one would miss out on the major
"fully corrected" processing advantages: more particles and better
movie alignments. Are you still with me? <br>
<br>
Bottom line: use the FRC as an immediate proof of the camera
correction and stop thinking about the issue henceforth. ;)<br>
<br>
By the way, the camera correction even improves the power spectrum
and thus the CTF determination... But that we will show in a
forthcoming publication!<br>
<br>
Cheers,<br>
<br>
Marin<br>
<br>
<br>
On 02/10/2018 13:03, Oliver Clarke wrote:<br>
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<div dir="ltr">Hi Marin,</div>
<div dir="ltr"><br>
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<div dir="ltr">Couldn’t you just extract the same final particle
set from both sets of micrographs (with/without a posteriori
gain correction) and refine, though, without going through the
whole pipeline independently for both? </div>
<div dir="ltr"><br>
</div>
<div dir="ltr">Knowing that it affects the quality of the final
density map would definitely be helpful, I think.</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">Cheers</div>
<div dir="ltr">Oli</div>
<div dir="ltr"><br>
On Oct 2, 2018, at 11:51 AM, Marin van Heel <<a
href="mailto:0000057a89ab08a1-dmarc-request@JISCMAIL.AC.UK"
moz-do-not-send="true">0000057a89ab08a1-dmarc-request@JISCMAIL.AC.UK</a>>
wrote:<br>
<br>
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Dear Dimitry,<br>
<br>
We have shown that you can perform movie alignments on a
more local basis without using very extreme low-pass filters
(sometimes described as "B-factors"). Thus you will
necessarily have a larger yield of usable particles from the
same set of micrographs. That is more than sufficient
evidence of improvement! The FRC is a metric that is local
to your correction operation and that measures the
improvement directly. The final 3D map resolution only comes
at the end of a long pipeline, that any two people will
perform differently and that is too indirectly related to
the very early data-set correction. Bottom line: the FRC
metric is necessary and sufficient to show the data-set
improvement by the camera correction. However it does not
necessarily and sufficiently guarantee that nobody will
generate gold-standard garbage further down the pipeline.
;)<br>
Cheers,<br>
Marin<br>
<br>
On 02/10/2018 07:54, Dimitry Tegunov wrote:<br>
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<div dir="ltr">Dear Marin,
<div><br>
</div>
<div>do you have results showing that the proposed
correction improves the final map resolution vs.
conventionally gain-corrected movies? I think the FRC
curves are necessary and sufficient proof , but not
sufficient to prove the advantage of your approach.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Dimitry</div>
</div>
<br>
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<div dir="ltr">On Mon, Oct 1, 2018 at 9:23 PM Marin van
Heel <<a
href="mailto:0000057a89ab08a1-dmarc-request@jiscmail.ac.uk"
moz-do-not-send="true">0000057a89ab08a1-dmarc-request@jiscmail.ac.uk</a>>
wrote:<br>
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<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Dear
Da,<br>
<br>
In IMAGIC-4D you can perform the necessary camera
correction! <br>
(<a href="https://www.nature.com/articles/srep10317"
rel="noreferrer" target="_blank"
moz-do-not-send="true">https://www.nature.com/articles/srep10317</a>).
It does it better than any <br>
manufactures correction and improves the data
significantly even when <br>
performed after using the standard gain correction.<br>
<br>
Cheers,<br>
<br>
Marin<br>
<br>
<br>
=====================================================<br>
<br>
On 01/10/2018 15:36, Da Cui wrote:<br>
> Hi all,<br>
> The gain reference image for one dataset was
missing by accident. In order to achieve a more accurate
motioncor result, does anyone have idea about how to
generate a gain reference image from the dataset (around
3k movies)?<br>
> Thank you so much for your help!!!<br>
> ---Da<br>
><br>
>
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