Bead Helper Plugin Help


This plugin is designed to assist in the speedy refinement of fiducial models - allowing you to quickly identify and correct bad points. "Bead Helper" is designed to compliment the functionality of "Bead Fixer" by providing useful visual aids and tools which can be used to rapidly rectify or delete bad contours - i.e. contours where the fiducial marker has tracked poorly. If tracking goes well you probably won't need Bead Helper, but in situations where tracking proves problematic Bead Helper has many tools which may be able to help.

Click here to see a video tutorial

Hot Key Summary
[e]           Moves (or adds) point in the current view to its expected position

[E]           Smooth current contour using the current settings under "Move points to expected position"
[f]            Fill all missing points (gaps) in the current contour between existing points using estimated positions
[F]            Fill all gaps in the current contour past the end points
[d]           Delete all points above or below the current point - whichever end is closer

[r]            Reduce the current contour to its original seed point

[h]           Go to the next biggest "hole" between seed points
[y]           Select point with the next biggest "y jump"
[b]           Select point with the next biggest distance from its estimated position
[w]          Select point with the next biggest weighted distance from its estimated position
[o]           Select next biggest contour using "Re-order Contour" criteria

[m]          Jump to middle view/seed point
[M]         Move current contour to different contour number
[q] or [u]       Toggle current contour checked/unchecked (checked contours are shown as stippled). WARNING: [u] can conflicts with 'undo' in LineTracker.
[U]          Toggle current point(s) checked/unchecked (checked points are shown as little spheres)
[I]            Print contour stats for current object
[Enter]    Go to next unchecked (unstippled) contour.

[mouse wheel]     Scroll through points and/or views

Visual Aids




I've found tracking >120 seeds is very slow (processing time increases exponentially), hence it's a good idea to start with 100, and if those track well you can add another 100.

It's best to have an even distribution of points, starting at the middle. To help achieve this use [h] and add the nearest isolated fiducial to the crosshair.

If particles are on both sides it's best to have a roughly even distribution, but if I'm adding >100 fiducials I find I usually get a pretty good spread by choosing randomly. The more careful approach is to use [pagedown] and [insert] to see if a fiducial is on the top/bottom and if looks easy to track. You can also click "More Actions" then "show fiducials on bottom as purple" to help see which contour are on which side.

For many tilt series beadtracker does an excellent job the first time, however tracking often go off course:
  1. when one fiducial passes close by another
  2. when consecutive views are poorly aligned
  3. when fiducials are obscured
Tracking is most likely to fail at high tilt where fiducials are often hard to see. When this happens the best course of action is to delete all points from these bad views then manually seed the first 5 or 10 contours and try "track fiducial model as seed" again.

If the first few fiducials track poorly, then chances are ALL the fiducials will track badly - so make sure the first few are correct before proceeding.

Fixing bad fiducials is slow - so don't hesitate to delete any contour which looks bad. For this reason it's a good idea to seed more fiducials than you need.

To check the tracking of each contour I highly recommend turning on "keep point centered" (the square button on the ZAP window) and toggle [t] to see the point more clearly. Use the [{] and [}] (or better yet the mousewheel) to iterate through point, [c] and [C] to iterate contours and the numpad keys to shift points.

For the best reconstruction it's a good idea to manually check all contours using this method, unfortunately that can be very slow, and so it's useful to instead use the visual aids to identify bad points/contours before moving to the "Fine alignment" step.

To avoid checking the same contour twice use [u] to mark a good contour as 'checked' (stippled) and [Enter] to iterate through the remaining unchecked contours.

A fast way to correct bad points before fine alignment is to use [y], [b] or [w] to jump the "next worst point" and use [e] to move it to it's expected point. To identify bad contours you can chose a sort criteria under "Reorder contours" and use [o] to move through the values in descending order.

Be very careful using the provided methods to fill in gaps and/or smooth contours by moving points. Cross-correlation never does a perfect job, and so often shifts between images are correct, and it's important you don't lose these. When first inspecting the fiducial model you should make a note of which views appear out of alignment.


This plugin was created by Andrew Noske (andrew.noske<at>gmail<dot>com).
If you encounter bugs please e-mail me before e-mailing the IMOD group (to reduce traffic).
In your e-mail please tell me exactly how and when the error/crash occurred and attach the model file you were using... enough information that I can replicate the error/crash.