Classification Matrix Image Files

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There are now two types of classification matrix files, those for 2-D image stacks and those for 3-D volume stacks. More 'layers' are used in the 3-D case because there are more alignment parameters.

These image files are normally produced by programs like or They contain information associating each of a set of particles with one or more reference particles, and by extension, 3-D orientations. They are generally produced (in some cases trivially) from a similarity matrix, by searching it for minimum (best matching) values. This file format permits each particle to (optionally) be associated with more than one reference image. The file normally contains a set of 6 images.

The first image in the file contains the classification information. The size of the image in y is the number of particles that have been classified. The size of the x-axis determines the maximum number of different references each particle can be associated with. Most often nx = 1, meaning each particle is associated with a single reference. While the pixel values (like all EMAN2 images) are floating-point, they actually contain integers indicating reference image number.

The file will normally contain 6 images for 2-D stacks:

Or 8 images for 3-D stacks:

EMAN2/ClassmxFiles (last edited 2011-03-16 16:19:55 by SteveLudtke)