[Chimera-users] colormap -and- opacity functions for voxels

Andrew Jewett aij at physics.ucsb.edu
Tue Mar 1 16:23:14 PST 2005

   Hi.  I've asked a lot of questions, and I keep getting these long
thoughtful and technical replies.  Thanks.  It's nice to get these replies
However don't feel obligated to reply at all, at least when I post a 
question.  The other features I mentioned are more important to me at 
least.  I don't want you to be kept busy replying to emails.

  The question is: why not have a simultaneous independent opacity-map and 
color-maps for voxel-rendering?  (...and I suppose, why do they have to be 
linear functions?  Is piecewise linear hard to implement?)

  It seems unnecessary that the voxel values should only determine
the opacity of the voxel.  It seems reasonable to allow the color to
be determined by the volxel value in addition to the opacity
(for example, a cold-to-warm-to-hot color scheme).

  It looks like some kind of colormap user interface has been implemented
in chimera.  (Nice T4-phage slab image, by the way..)  Would this be hard?
This way, one could distinguish the DNA inside the T4 phage from the 
within capsid shell.

Currently, 3-D volumetric rendering is cool, but it needs ...something.

   Since the demand for voxel rendering is probably low,
I would understand if you choose to delay to ignore these issues.


------- That's the end of my question, but I included
------- some pictures at the end, for comparison.
------- You can skip this part.
------- They are not in color, but they do look ...pretty.
------- I wonder what they are doing?


   Probably the main reason it looks so nice I think is because their 
data is manifestly much less bumpy than electron microscopy data.  Also 
I'm suspect that increadibly expensive 3-D hardware doesn't hurt either.
However there is something else interesting going on in these pictures.
It seems that what appear to be fully opaque objects have
a range of brightnesses/colors.  In chimera, fully opaque objects
are solid white (or blue or whatever color is set by the user)
and they have no features except their somewhat fuzzy silhouette.

   The source of these pictures is a paper published at:

   One thing they talked about in the article was that they use
separate brightness and opacity functions as a function of voxel
value.  They also use more general piecewise-linear functions
instead of linear ones ("percentage classification").
The combination of those two features might explain something.
Anyway, I wonder what they are doing.

No need to reply.  I'd rather you work on other stuff right now.



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