Tomography operations are activated by selecting the "Micrograph/Tomography" menu item or the tomography tool (Dot icon). This brings up a new window with a menu "Tomography" and parameters:

• Tomography
  • Set tilt angles - opens a dialog box called "Tilts" to set a tilt series giving the start angle and the constant increment.
  • Read tilt angles file - reads a *.rawtlt file as generated by some tomographic acquisition packages.
    
  • Find markers in current image - automatically find markers (uses the "Gold radius" parameter).
  • Generate markers from seed - calculates a model and missing markers.
  • Renumber markers in current image - ensure contiguous marker numbering.
    
  • Extract markers - extracts all fiducial markers into a multi-image file for further processing.
  • Refine alignment - opens a dialog box for refining micrograph orientations.
  • Show marker table - opens the marker table window.
  • Delete selected markers - deletes all selected markers.
  • Delete selected markers in all images - deletes selected markers in all micrographs.
  • Delete all markers - delete all markers in memory (no recovery!).
  • Close - close window and deactivate tomographic operations.
• Parameters
  • Radiobuttons to display/hide markers, errors and labels.
    
  • Marker radius - sets the radius for fiducial markers used for drawing circles and finding markers by cross-correlation.
  • Markers - indicates the number of gold markers and a button to show the marker table.
  • Selected -  indicates the currently selected marker and its figure-of-merit.
  • Residual - shows the latest calculated marker location resdiual.
  • Tilt axis - tilt axis defined as an angle of rotation from the x-axis.
  • Tilt angles - an editable list of image numbers and tilt angles (these can be set using the menu item "Tomography/Set tilt angles").

Setup for tomography

The tilt series must be read into bshow as a multi-image file (PIF, Spider or Imagic formats). Next the gold radius in pixels is set, followed by the tilt axis angle. The tilt axis angle is defined with respect to the x-axis and must be known to within a degree. The tilt angles can be read from a text file with a list of angles ("Read rawtlt file" menu item), or can be set using the "Set tilt angles" menu item.

Picking seed fiducial markers

To pick the initial fiducial markers, go to the zero-degree tilt micrograph and use the "Tomography/Find markers in current image" menu item. A synthetic disk based on the gold radius is used to find markers by cross-correlation, which may take several seconds. A dialog box then opens with two sliders for selection of markers. The top slider allows the user to select a FOM cutoff while the bottom slider allows the user to eliminate markers close to the micrograph edge. Once these parameters have been selected, click on the "Done" button.

Correcting marker positions

Markers can be picked (when the tomography tool is selected) and positioned individually, or all the markers in the current micrograph can be moved together when the second tomography tool (multiple dots icon) is selected.

Jumping to significant markers

The marker table can be opened from the "Marker table" button or using the "Tomography/Show marker table" menu item. The buttons can be used to jump to the smallest ("|<"), next largest ("<"), next smallest ">"), or largest (">|") marker with respect to its residual or FOM. The FOM's are the correlation coefficients for the markers generated during tracking or position refinement.

Mouse controls for marking

The mouse behavior depends on the tool selected:

Pointer tool:

• Left/middle button:             move a marker
• Shift - left/middle button:    delete a marker

Clicking the left or middle mouse button in a marker grabs it for dragging.
To delete a marker, hold down the shift key and click the left or middle button on the marker.

Marker tool:

• Left/middle button:             create or move a marker
• Shift - left/middle button:    delete a marker

Clicking the left or middle mouse button in a marker grabs it for dragging.
Clicking the left or middle mouse button in an empty region on the image creates a new marker.
To delete a marker, hold down the shift key and click the left or middle button on the marker.

Multiple markers tool:

• Left/middle button:             select region or move selected markers

Clicking the left or middle mouse button in a marker grabs all selected markers for dragging.
Clicking the left or middle mouse button in an empty region and dragging it creates a rectangle within which all markers are selected. The selected markers can then be dragged by grabbing one of them.

Reading and saving tomographic parameters

The "Micrograph/Read parameters" and "Micrograph/Write parameters" menu items are used to read and write parameter files (usually in the STAR format).

Bernard Heymann 20100216