[Chimera-users] Volume segmentation question

Tom Goddard goddard at cgl.ucsf.edu
Mon Jun 4 11:35:40 PDT 2007

Hi Toby,

  Chimera does not have very useful tools for segmenting EM tomography 
although we would like to develop such tools.  The pick surface pieces 
tool seems quite limited because it only works with connected contour 
surfaces.  Just varying contour level does not give you much control.  
It would be possible to improve that tool as you suggested so that it 
copies the enclosed voxels to a new map, or sets the enclosed voxels to 
zero.  I have some doubts that that would be useful.  If you have to 
raise the contour level to break undesired connections, then you won't 
get a copy of the data out to low enough threshold levels around the 
pieces you choose.

  A couple tools that can help with segmentation are volume eraser, and 
zones in volume viewer.  Volume eraser lets you set to zero map values 
within (or outside) a sphere that you can move around and resize.  You 
can save the resulting map to a new file with volume dialog menu entry 
File / Save map as.... 


The volume dialog menu entry Features / Zone lets you show only parts of 
map within a radius of selected markers.  Using volume dialog File / 
Save map as... will then save just the shown zone with zeros outside the 
given radius.


Sometimes you want zones around volume path tracer links, not just 
around markers.  The undocumented bondzone command allows this.  It is 
described below.

The guide to volume data display describes other capabilities:


  Many labs use the commercial program Amira to segment EM tomography.  
You paint regions in individual data planes to delineate structures in 
the map.


Thomas Goddard wrote:
> Hi Manfred,
>   I added the capability to segment out density around paths
> created with the Chimera path tracer tool.  Formerly the zone
> capability only segmented density near marker positions, and not
> the connecting links.  The new capability works by using closely
> spaced points placed along the links that join markers.  Besides
> the volume dialog zone tool and equivalent surface zone tool
> (menu entry Tools / Surface & Binding Analysis / Surface Zone)
> the color zone tool (menu Tools / Volume Data / Color Zone)
> can now color the density surfaces near path tracer links.
>   This new feature is in Chimera version 1.2255.  I did not figure
> out a good place to put the option in the dialogs and instead made
> a Chimera command, called "bondzone" to enable segmenting and coloring
> around links (also called "bonds").  The feature is currently not turned
> on by default.  You type the command
> 	bondzone
> to the Chimera command entry field.  To show the command entry field
> at the bottom of the main Chimera window use menu entry Favorites /
> Command Line.  After typing this command the volume dialog zones,
> surface zone dialog, and color zone dialog all will use extra points
> (not displayed) along selected links.  The spacing of the extra points
> is relative to the radius of the link cylinder.  By default the points
> are spaced along the link separated by one link radius.  You can change
> this using the bondzone command with a numeric argument.  For example,
> 	bondzone 0.5
> will cause all subsequent segmenting and color zones to use points
> spaced at 0.5 times the radius of the link.
>   Note that only *selected* bonds and atoms are used by the zone
> tools.  I added a new keyboard 2-key shortcut "sc" that extends
> the current selected atoms or bonds to all connected atoms and
> bonds.  So you can click on one marker in a path tracer trace,
> then type sc to select all connected markers.  Recall that to
> turn on keyboard shortcts you use menu entry Tools / General
> Controls / Accelerators On.  They can be set on by default using
> the Prefereces dialog, Tools category.  You can also press the
> up arrow key on the keyboard to extend a selection to all traces
> (connected or not) in the same path tracer "marker set".
>   If you want to turn the "bondzone" feature off so you get zones
> only around selected markers use command:
> 	~bondzone
> The tilde (~) in front of Chimera commands often means undo the
> normal command effect.  When you turn bondzone on or off this is
> saved in your Chimera preferences file (~/.chimera/preferences)
> so that the setting remains the same when you next start Chimera.
>   Would be nice to not have to mess with this bondzone command and
> just have that be the default behaviour but it is currently pretty
> inefficient (ie slow) and I did not want to impair performance when
> taking a zone around a 10,000 atom crystal structure fit into a density
> map.  Hopefully I can improve the performance in the future and make
> this zone behaviour the default.
>   Thanks for suggesting this capability.
> 	Tom

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