[3dem] [ccpem] K-means clustering algorithm

[Marin van Heel]

Dear Leonardo,

You may want to go to the original literature to better understand the 
basic principles of classification. In our recent review 
(http://www.scirp.org/journal/PaperInformation.aspx?PaperID=70260) you 
will also find the links to our original classification papers from the 
1980s. Things got rather messed up in terms of nomenclature in the 
literature recently because people now often refer to "2D 
classification" while actually referring to a mixture of reference-based 
alignments and automatic classification. The same happens in"3D 
classification". I have also discussed some of these issues in my Wiley 
2017 award lecture which you can find on line. These issue are discussed 
in more depth in a methodological paper that will appear shortly in 
IUCrJ (www.iucrj.org).

Cheers,

Marin

================================================


On 18/08/2017 08:05, Leonardo Feletto wrote:recently
> Dear all,
>
> I am a newbie in using image analysis softwares and in studying image analysis in general. I was reading this review
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409659/
>
> 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:
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409659/figure/F3/
>
> 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.
>
> I hope someone could answer my questions,
>
> Best regards
>
>
> Leonardo


-- 
==============================================================

     Prof Dr Ir Marin van Heel

     Laboratório Nacional de Nanotecnologia - LNNano
     CNPEM/LNNano, Campinas, Brazil

     tel:    +55-19-3518-2316
     mobile  +55-19-981809332
                  (041-19-981809332 TIM)
     Skype:  Marin.van.Heel
     email:  marin.vanheel(A_T)gmail.com
             marin.vanheel(A_T)lnnano.cnpem.br
     and:    mvh.office(A_T)gmail.com

--------------------------------------------------
     Emeritus Professor of Cryo-EM Data Processing
     Leiden University
     Mobile NL: +31(0)652736618

     Emeritus Professor of Structural Biology
     Imperial College London
     Faculty of Natural Sciences
     email: m.vanheel(A_T)imperial.ac.uk

--------------------------------------------------

I receive many emails per day and, although I try,
there is no guarantee that I will actually read each incoming email.