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Microtubule Seam-search

Microtubule seam-search is very important to separate α- and β-tubulins.

What the seam-search algorithms in cylindra do is simply adding a new column named "isotype-id" to the molecules features. As seam-search is usually combined with subtomogram averaging and alignment, these methods are located in the STA widget.

Seam-search Based on Cross-correlation

API: seam_search

GUI: STA widget > Analysis > Seam search > Seam search by correlation

Although the structure of α/β-tubulins are very similar, it is known that trying all the possible patterns and comparing the cross-correlation is useful to distinguish them.

Seam search

List of parameters
  1. "layer" is the molecules layer to be seam-searched.
  2. Set the template image and mask parameters in the STA widget.
  3. "anti-template path" is the path to the anti-template image.
  4. "interpolation" is the interpolation method used for resampling the sub- volumes.
  5. "npf" is the number of protofilaments. If molecules are created in cylindra, this value should already be determined by CFT.
  6. You can select how to (or not to) show all the averages for different seam locations by the "show averages as" combobox.
  7. "cutoff" is the relative cutoff frequency of the low-pass filter. This value is usually smaller than the value used for subtomogram alignment.

Molecules labeled with 0 are the molecules that should be considered as the template, and 1 the anti-template.

API: seam_search_manually

GUI: STA widget > Analysis > Seam search > Seam search manually

This method labels the molecules by the given seam location. location=0 will label molecules with

[0, 0, ..., 0,
 1, 1, ..., 1,
 0, 0, ..., 0,
 1, 1, ..., 1,]

and location=1 will label molecules with

[1, 0, ..., 0,
 0, 1, ..., 1,
 1, 0, ..., 0,
 0, 1, ..., 1,]

Seam-search by Features

API: seam_search_by_feature

GUI: STA widget > Analysis > Seam search > Seam search by feature

This method labels the molecules by the given feature. The feature should be such that approximately label the α- or β-tubulins. Usually, molecules should be labeled by classification using microtubule-associated proteins as the fiducials.