<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body dir="auto">
I guess you still have to define what R is😊<br>
<br>
<div id="AppleMailSignature" dir="ltr">Regards,
<div>Pawel</div>
</div>
<div dir="ltr"><br>
On Dec 4, 2018, at 4:56 PM, Carlos Oscar S. Sorzano <<a href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<p>Dear Marin,</p>
<p>thank you for the reminder, since I had certainly forgotten. What you call a contrast reversal is most likely a nomenclature issue. If you have two images, I_observed and I_ideal, and the relationship between the two is simply a multiplicative term</p>
<p>I_observed = H I_ideal</p>
<p>exactly the same relationship is described by the relationship (assuming there are no zeros)<br>
</p>
<p>F I_observed = I_ideal</p>
<p>The relationship between F and H is F=1/H, which implies a contrast reversion. I have explictly avoided G to denote any of these two images (F or H) to avoid confusions. Which of the two is called "gain" is a matter of definition. I prefer describing H as
the gain, but I understand other people may prefer the other option.</p>
<p>Regarding R^2, it is true I did not define it assuming it was general knowledge. It is a very standard statistical measure of quality called the coefficient of determination (<a class="moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Coefficient-5Fof-5Fdetermination&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=nYF1wmtGLXiMY93v2J7Kd4Eq6UmjU-dbkYDbd0-hMFU&e=">https://en.wikipedia.org/wiki/Coefficient_of_determination</a>),
and it expresses the fraction of the original variance explained by a model. If R^2=1, the model has totally explained the original variance, while if R^2=0, the model explains the same variance as the mean of the observations, which is the simplest, sensible
model we could have.</p>
<p>Cheers, Carlos Oscar<br>
</p>
<div class="moz-cite-prefix">El 04/12/2018 a las 21:48, Marin van Heel escribió:<br>
</div>
<blockquote type="cite" cite="mid:CAHgnXPXmP2zUNa1J_p0v4JZ9onvVsQ2MpANtdLLpzw4Hy1A3DA@mail.gmail.com">
<div dir="ltr">
<div dir="ltr">
<div>Hi Carlos Oscar! <br>
</div>
<div>I just remembered I had posed a question about your camera normalisation paper (
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pubmed_29551714&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=GbJK0WJKZBqEfGERNJc2mspMIWIiDrX5-tdTkJL6Fnw&e=" rel="noreferrer" target="_blank" moz-do-not-send="true">
https://www.ncbi.nlm.nih.gov/pubmed/29551714</a>.) on this site some two months ago, in which you critisized our 2015 camera normalisation paper (<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_srep10317&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=V-yc_wFNb5n9w2eVCBL9uP-MzMmoxOdcVYCzjqm9fp4&e=" moz-do-not-send="true">https://www.nature.com/articles/srep10317</a>).
Did you already respond to my question and I missed your answer? <br>
</div>
<div><br>
</div>
<div>Cheers</div>
<div>Marin<br>
</div>
<div><br>
</div>
<div>My question was:</div>
<div><br>
</div>
<div>QUOTE:<br>
</div>
<div>What you call our "gain image" is - apart from an erroneous contrast reversal - actually more similar to the "official" gain image in your Fig 1 than does the one generated with your proposed algorithm. I would be interested in knowing what the R2 turns
out to be after you correct the contrast reversal since it visually is better than yours. It would be nice if you could respond to this mailing including that information!? By the way how exactly is this R2 metric defined (I could not find it anywhere in the
paper)? <br>
</div>
<div>END QUOTE<br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Tue, Oct 2, 2018 at 10:21 PM Marin van Heel <<a href="mailto:marin.vanheel@googlemail.com" moz-do-not-send="true">marin.vanheel@googlemail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<div class="gmail-m_-1407481537373201022moz-cite-prefix">Dear Carlos Oscar and Dimitry,<br>
<br>
Unfortunately, you seem to have missed the point of our Afanasyev 2015 paper. Our paper does not try to duplicate the "experimentally determined Gain image" but tries to normalize the signal from each pixel to the same average and the same standard deviation
at the exposure and contrast level that the data set was recorded. Our approach typically improves significantly on standard "<i>a priori</i>" flat field/gain corrections.<br>
<br>
We are not directly interested in generic "gain images" as such and we certainly do not generate "gain images" that have an inverted contrast when compared to the other ones you have in Figure #1 of your paper. Your comments on our methods are thus not appropriate:
"<i>T</i><i>o the best of our knowledge, the only article that addresses a similar problem is that of Afanasyev
</i><i>et al.</i><i> (2015). In their work, they assimilate the gain of the camera to the standard deviation of each pixel over a large number of movies, and they prove this is a successful way of identifying dead pixels. However, our results show that this
approach does not provide a consistent gain estimation (Fig. 1)</i>."<br>
<br>
What you call our "gain image" is - apart from an erroneous contrast reversal - actually more similar to the "official" gain image in your Fig 1 than does the one generated with your proposed algorithm. I would be interested in knowing what the R2 turns out
to be after you correct the contrast reversal since it visually is better than yours. It would be nice if you could respond to this mailing including that information!? By the way how exactly is this R2 metric defined (I could not find it anywhere in the paper)?
<br>
<br>
I would want to suggest you and your colleagues to use the FRC metric to prove that your approach does indeed remove the influence of the various patterns of your detectors exhibits.<br>
<br>
My two cents<br>
<br>
Marin<br>
<br>
=====================<br>
<br>
<br>
On 02/10/2018 15:19, Carlos Oscar Sorzano wrote:<br>
</div>
<blockquote type="cite">By the way, in our article we compared both methods (ours and Marin).
<br>
<br>
Kind regards, Carlos Oscar <br>
<br>
<br>
On 01/10/2018 21:23, Marin van Heel wrote: <br>
<blockquote type="cite">Dear Da, <br>
<br>
In IMAGIC-4D you can perform the necessary camera correction! (<a class="gmail-m_-1407481537373201022moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_srep10317&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=V-yc_wFNb5n9w2eVCBL9uP-MzMmoxOdcVYCzjqm9fp4&e=" target="_blank" moz-do-not-send="true">https://www.nature.com/articles/srep10317</a>).
It does it better than any manufactures correction and improves the data significantly even when 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>
<blockquote type="cite">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>
######################################################################## <br>
<br>
To unsubscribe from the CCPEM list, click the following link: <br>
<a class="gmail-m_-1407481537373201022moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCPEM-26A-3D1&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=yT3kjQpRGyp5cKZEwjnWpMpmpVgZ4oGFbYclNxESB2M&e=" target="_blank" moz-do-not-send="true">https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1</a>
<br>
</blockquote>
<br>
<br>
</blockquote>
<br>
</blockquote>
<p><br>
</p>
<pre class="gmail-m_-1407481537373201022moz-signature" cols="72">--
==============================================================
Prof Dr Ir Marin van Heel
Laboratório Nacional de Nanotecnologia - LNNano
CNPEM/LNNano, Campinas, Brazil
tel: +55-19-3518-2316
mobile +55-19-983455450 (current)
mobile +55-19-981809332
(041-19-981809332 TIM)
Skype: Marin.van.Heel
email: marin.vanheel(A_T)<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=ZQzkqvtzk56LQirMk_M_H7faPSmvycM_1nEcCV6dkxI&e=" target="_blank" moz-do-not-send="true">gmail.com</a>
marin.vanheel(A_T)<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lnnano.cnpem.br&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=tvzbuokQ-c7H8ClCHLw_SKUYf6T2mQVycJEj9nQ3_vA&e=" target="_blank" moz-do-not-send="true">lnnano.cnpem.br</a>
and: mvh.office(A_T)<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=ZQzkqvtzk56LQirMk_M_H7faPSmvycM_1nEcCV6dkxI&e=" target="_blank" moz-do-not-send="true">gmail.com</a>
--------------------------------------------------
Emeritus Professor of Cryo-EM Data Processing
Leiden University
Mobile NL: +31(0)652736618 (ALWAYS ACTIVE SMS)
--------------------------------------------------
Emeritus Professor of Structural Biology
Imperial College London
Faculty of Natural Sciences
email: m.vanheel(A_T)<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__imperial.ac.uk&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=xjNoEFFbWleDIHeBdgmnx4pQ3hWrS4DA9L09cGZ7fX8&e=" target="_blank" moz-do-not-send="true">imperial.ac.uk</a>
--------------------------------------------------
I receive many emails per day and, although I try,
there is no guarantee that I will actually read each incoming email. </pre>
</div>
</blockquote>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano e-mail: <a class="moz-txt-link-abbreviated" href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>
Biocomputing unit <a class="moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__i2pc.es_coss&d=DwMDaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=e4rYqG-wlLmE48eJd2mVvUW7P2JP8xA6uSYQ7Q41j-k&e=">http://i2pc.es/coss</a>
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510
28049 MADRID (SPAIN) Fax: 34-91-585 4506
------------------------------------------------------------------------
</pre>
</div>
</blockquote>
<blockquote type="cite">
<div dir="ltr"><span>_______________________________________________</span><br>
<span>3dem mailing list</span><br>
<span><a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a></span><br>
<span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=Fnm7k8NmR1cuxq4VkEc5oznU31Aryw9_ULlCEVqzpC8&e=">https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=BmtVdlQoD6zHW2o25IZa6vGz0lwSvq24Wch-T3W-Tcw&s=Fnm7k8NmR1cuxq4VkEc5oznU31Aryw9_ULlCEVqzpC8&e=</a></span><br>
</div>
</blockquote>
</body>
</html>