Cross correlation matrix

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The cross correlation matrix (often called ccmatrix in Dynamo jargon) of a set of N particles is an N X N matrix. Each entry (i,j) represents the similarity of particles i and j in the data set.

Definition of similarity

This similarity of particles i and j measured in terms of the normalized cross correlation of the the two aligned particles, filtered to their common fourier components, and restricted to a region in direct space (indicated by a classification mask). The pseudo code will run as:

  1. read particles i and j -> pi, pj
  2. align particles i, and j -> Aipi, Ajpj
  3. compute missing wedges for particles i and j -> Wi, Wj
  4. rotate missing wedges -> RiWi, RjWj
  5. compute Fourier coefficients common to bCoth rotated missing wedges

Cij = intersection(RiWi, RjWj)

  1. filter pi with Cij
  2. compare the filtered particles inside the classification mask.


Input of a ccmatrix

Computation of ccmatrix

Application of a ccmatrix