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, or to contours with high mean 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


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 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:

Contour Mode

This mode lets you move to contours with the highest mean residuals. With a fiducial model, you can step through all the points in such contours and adjust ones as needed, or choose to delete the whole contour. With a model based on local patch tracking by Tiltxcorr, you can delete the contours where the tracked positions are least consistent with the overall fit. In addition to the buttons to read a log file and run Tiltalign, this mode has the following controls:

Moving All Points by Residual

The guiding principle when deciding whether to move one or many points by residual is that model points should not be moved away from the gold particles. If many points are displaced from their proper location, this will lead to a poorer alignment of the views where such points are located (typically the high tilt views).

The robust fitting now available in Tiltalign is a more statistically valid method of eliminating or down-weighting points with high residuals than blindly moving points by the residual values from a fit that includes all the points with equal weight. The robust fitting should produce a better estimate of the true alignment solution. Nevertheless, more experience with this method is needed to confirm this, so here are some guidelines for moving large numbers of points by their residuals:

  1. To avoid misaligning high tilt views, where residuals tend to be higher, in favor of the lower tilt views, you should have the large residuals be selected relative to other residuals on nearby views. Do this by choosing Neighboring views rather than All views in the Residual Reporting box in Etomo.
  2. You should always go through enough points manually so that you can become confident that the large majority of points are being moved correctly. If you are just doing global alignments, perhaps do one round manually after switching to reporting residuals relative to neighboring views. If you have a small number of local areas, perhaps do one complete round through all of them manually. If you have many local areas, perhaps examine the first few points in each local area by hand to see that the suggested movements are appropriate, then move the rest in that area automatically. On the next round, you could then move points in all areas automatically.
  3. If you know that you are going to be using local alignments, do not move points by the global residuals automatically, as it is quite likely to move model points off of the gold. Do the automatic refinements only with local residuals.

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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