[Chimera-users] multi-channel solid rendering
goddard at sonic.net
Tue Apr 29 22:35:13 PDT 2014
Yes, Chimera does not correctly blend two overlayed transparent models, so blending “solid” style (ie volumetric) density map display of 2 or more maps does not blend the colors. Usually one map simply covers the other one.
I’ve put a script blend.py on the Chimera Python scripts web page
that blends 2 or more maps (actually simply adds the red,green,blue,opacity values pointwise). For example
runscript /Users/goddard/blend.py #1-3 #4
will add the solid-style colors currently shown for maps #1, 2 and 3 creating a model #4. Then I’d want to hide #1-3 to show only #4:
The created model #4 is not a density map, it is a volumetric model, so it will not appear in the volume viewer dialog, only in Model Panel. It will not automatically update if you change the map colorings. After you update the map colorings, or map region displayed, you would have to show those maps (so the new colors actually get computed), then rerun the blend.py script. You can use the same model #4 when you rerun the script and it will reuse that model. I’m not sure this script will help you, it is a cumbersome process to show the blended colors. I tested it in Chimera 1.9 (release candidate).
Maybe blending of solid style map colors will be put back into Chimera 2. It certainly would if we decide to support optical microscopy where imaging multiple fluorescent labels is common. Currently our Chimera 1 target audience is electron microscopy where multi-channel imaging is almost never done. Such new developments are probably at least a year away.
On Apr 29, 2014, at 1:36 PM, Nick Walter wrote:
> I've been attempting to create a movie in Chimera using multiple data files in solid style volume rendering, and I have been running into an issue where Chimera consistently shows the last channel to be loaded on top, regardless of the spacial position of the data with respect to the other solid channels. I found this message (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006329.html) which explains that multi-channel solid rendering was removed in 2008. I was wondering, if there are any plans to reinstate this feature, or if you were aware of any work-arounds that would work well for creating movies.
> Thank you for your time,
> Nick Walter
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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