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<div class="">Dear Leonardo,</div>
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<div class="">you are correct. Somehow the effort to make the text as brief as possible resulted</div>
<div class="">in elimination of some definitions. </div>
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<div class="">CCC means correlation coefficient, that is a number that reflects similarity of two</div>
<div class="">images computed without changing their orientations.</div>
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<div class="">ccf means cross-correlation function, i.e., so to say a collection of correlation coefficients computed</div>
<div class="">for various orientations of an image with respect to the template. Further, the cryptic</div>
<div class="">text in Figure 3 “Calculation of 2D ccfs (psi, s_x, s_y)” is meant to say that</div>
<div class="">crosscorrelation functions are computed between 2D image with respect to a set of possible</div>
<div class="">angles and shifts (translations) with respect to a template, so of course resulting ccfs are 3D, i.e., functions of three</div>
<div class="">variables: in-plane angle and two translations.</div>
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<div class="">As for exact details of RELION implementation, they would be better explained by the author.</div>
<div class="">However, as we argue in the Supplement of the Primer, ML-based clustering can be seen as a generalization</div>
<div class="">of simple K-means algorithm or, vice versa, K-means as a simplification of ML method.</div>
<div class="">The cited reference (it is available on the net and can be read in a browser):</div>
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<div style="margin: 0px; line-height: normal;" class=""><font face="Helvetica" class=""><span style="font-size: 14px;" class="">MacKay, D.J.C. (2003). Information Theory, Inference and Learning Algorithms</span></font></div>
<div style="margin: 0px; line-height: normal;" class=""><font face="Helvetica" class=""><span style="font-size: 14px;" class="">(Cambridge, Cambridge University Press).</span></font></div>
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<div class="">gives very good and accessible introduction to clustering, mixture of gaussian approach and other</div>
<div class="">related matters and in particular contains a discussion why some ML-based methods</div>
<div class="">result in possible numerical instabilities.</div>
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Regards,<br class="">
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— <br class="">
Pawel A. Penczek, Ph.D.<br class="">
Professor<br class="">
Structural Biology Imaging Center, Director<br class="">
The University of Texas<br class="">
phone: 713-500-5416<br class="">
fax: 713-500-0652<br class="">
<a href="https://med.uth.edu/bmb/faculty/pawel-a-penczek/" class="">https://med.uth.edu/bmb/faculty/pawel-a-penczek/</a></div>
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On 18/08/2017 08:05, Leonardo Feletto wrote:recently<br class="">
<blockquote type="cite" class="">Dear all,<br class="">
<br class="">
I am a newbie in using image analysis softwares and in studying image analysis in general. I was reading this review<br class="">
<br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4409659_&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=t9ZXDtQrl9QMgRm6rtu3KOmfgGfANoF2gy-Y85iHp8o&s=6H13u1mmxerE4Uy16QwLju4qdAqRxSp0wfV08DXhHAU&e=" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4409659_&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=t9ZXDtQrl9QMgRm6rtu3KOmfgGfANoF2gy-Y85iHp8o&s=6H13u1mmxerE4Uy16QwLju4qdAqRxSp0wfV08DXhHAU&e=</a>
<br class="">
to better understand the k-means clustering algorithm, which underlies many processes in image analysis. I had some troubles to properly figure out something in this figure:<br class="">
<br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4409659_figure_F3_&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=t9ZXDtQrl9QMgRm6rtu3KOmfgGfANoF2gy-Y85iHp8o&s=QBc07-QzTd_Upp0zfhK0Sjl83ZwWDRjrSHi5n7wSN2Y&e=" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4409659_figure_F3_&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI&m=t9ZXDtQrl9QMgRm6rtu3KOmfgGfANoF2gy-Y85iHp8o&s=QBc07-QzTd_Upp0zfhK0Sjl83ZwWDRjrSHi5n7wSN2Y&e=</a>
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I cannot understand the meaning of CCCs and ccfs abbreviations used to describe the processes taking place while k-means clustering algorithm is running. In addition, I was interested to understand whether 3D classification in RELION relies on a variation of
this process too, integrating bayesian approach to correctly split the particles dataset in the different models eventually produced.<br class="">
<br class="">
I hope someone could answer my questions,<br class="">
<br class="">
Best regards<br class="">
<br class="">
<br class="">
Leonardo<br class="">
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