[Chimera-users] volume planes tool

Tom Goddard goddard at cgl.ucsf.edu
Wed Aug 13 19:11:21 PDT 2008

Hi Jeff,

  I don't think I will work on arbitrary orientation volume slice planes 
until I improve speed of flipping through axis aligned planes.  Here are 
some comments to give you a better idea of the issues.

  It is currently possible to get arbitrary volume planes in two ways, 
using the Resample button in the subregion selection panel, or the 
TomoPlane Chimera extension from Karen Gross and Christophe Best.  Both 
of these approaches are somewhat clunky.  The resample button requires 
you to press a button to get an updated view and creates a new volume on 
every press.  The TomoPlane tool is rather slow to update and has too 
complex a user interface and does not work with the latest Chimera (I'll 
fix that soon).  The main problem is performance and user interface.  
Axis aligned plane display with the volume dialog planes panel is a 
factor of several times slower than I'd like.  Improving rendering speed 
when changing the plane will probably be achieved by not destroying the 
plane model with each new orientation, using texture rendering (not done 
by TomoPlane), preloading full data, using 3-d opengl textures when the 
graphics card has sufficient memory.  The user interface should be 
simple, but it seems it will need another mouse mode to move the plane, 
and maybe some ability to have more than one plane, maybe show exact 
plane parameters (axis or angles), maybe allow marker placement on 
tilted planes.  Would make sense to put these parameters in the current 
volume plane panel, but those planes do not require a separate volume 
model.  The titled plane will need to be a separate model from the 
original volume.  The optimization and user interface problems are 

  I think improving the current axis-aligned plane rendering speed is 
more important.  Also think reducing volume memory use in "solid" mode 
is more important.  Also think volume mask support is more important.  
Plus there are quite a few other less closely related projects that I 
think have higher priority.  All this means that improved support for 
tilted cut planes isn't likely to get much attention for at least 
several months.


Jeff Triffo wrote:
> hi folks,
> anyone know if the volume plane tool will support arbitrary orientation 
> of the plane any time soon?
> -Jeff

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