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 rawtlt file - reads a *.rawtlt file as generated by
some tomographic acquisition packages.
- Find markers in all images - automatically find markers (uses the "Gold radius" parameter).
- Find markers in current image - automatically find markers (uses the "Gold radius" parameter).
- Renumber markers - ensure contiguous marker numbering.
- Extract markers - extracts all fiducial markers into a multi-image file for further processing.
- Delete all markers - delete all markers in memory (no recovery!).
- Close - close window and deactivate tomographic operations.
- Parameters
- Gold radius - sets the radius for fiducial markers used for drawing circles and finding markers by cross-correlation.
- Gold markers - indicates the number of gold markers.
- Selected - indicates the currently selected marker and its figure-of-merit.
- Radiobuttons to display/hide markers, errors and labels.
- 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.
Mouse controls for marking
- Left/middle button: create a marker
- Shift - left/middle button: delete a marker
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.