Bead Fixer Special Module

This module provides several functions to help generate tilt series fiducial models. It has an autocentering capability, so that an added point will be centered on the nearest fiducial. It has an option when generating the seed model which will automatically start a new contour for each point when appropriate. It has a function for finding the next gap or untracked place in the model and making that be the current point. It also will read the log file from running Tiltalign and move to points with high residuals. In addition, this module can be used to examine contours with values, adjust a threshold, and delete contours below the threshold.

Hot Key Summary

Controls

Toggle the pin button on to keep the Bead Fixer window on top of other windows.

The Operation radio buttons select the mode of operation; only the controls relevant to an operation will be shown. The three modes of operation are making a seed model, filling gaps in a tracked model, and fixing big residuals.

Autocentering

Autocentering is available when making a seed model, where it can be quite useful. It is also available when filling gaps but is much less likely to be useful there, except when tracking a long sequence of missing points. Turn on Autocenter and set the Diameter spin box to the average bead diameter (in pixels) to use autocentering. In this mode:

Seed Model Mode

This mode has the following features:

Gap Filling Mode

This mode provides controls for finding the gaps in the model, so that you can fill them if appropriate.

Residual Fixing Mode

This mode lets you correct bead positions that give large alignment arrows. It has the following features and controls:

Seed Model Mode with Contour Values

If any objects in the model contain stored values (e.g., correlation peak strengths for beads selected by Imodfindbeads), then in seed mode the dialog will have additional controls for setting a threshold and deleting points below threshold.

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