[Chimera-users] Using Chimera to look at confocal data

Tom Goddard goddard at sonic.net
Wed May 4 11:06:31 PDT 2011

Hi Tom,

   Chimera solid style volume rendering doesn't handle multi-channel 
images.  It doesn't know how to blend the colors from the different 
channels.  Chimera used to do this but I removed the code in 2008 
because it was too complicated.  If you use a really old version of 
Chimera it could work, although I think the only way to open a 
multi-channel data set was to use Priism format.  I removed that code 
because supporting multiple channels was too complex so it made it hard 
to improve the code for single channel volume data (electron microscopy) 
which is by far the most common use in Chimera.

   Here is one trick that will let you blend multiple channels for a 
single displayed plane (attached image is an example).  If you have two 
channels with Chimera model id numbers #0 and #1, then shift the origin 
of one volume so it is slightly in front of the other, for instance, set 
the "origin index" to "0 0 -1" for volume #1 using the Features / 
Coordinates tab of the volume dialog.  Then make the volume in front 
very transparent (Features / Brightness and Transparency).  Chimera 
renders the volumes in id number order and after it draws one solid 
style volume you won't see anything for a later one drawn behind (or at 
the same depth) as the first.  But if you put it slightly in front it 
will be shown.  This only works for a single plane unless you shift the 
second volume so the whole thing is in front of the first volume.  If 
you do that you'll want to use orthographic projection (Tools / Viewing 
Controls / Camera) otherwise the volumes won't even superimpose due to 

   While the above hack might be ok for making an image, I'd say Chimera 
is simply not useful for multi-channel volume data if you need 
solid-style rendering (which you most always do for noisy data).  
Multi-channel with surface style works.


> Hi,
> I've been using Chimera for a few years now to look at electron 
> tomography data and I have to say I think the software is absolutely 
> superb.  Recently I have started looking at 3D-confocal data and I 
> discovered with a bit of work I can open the data using chimera.  I 
> open each colour channel as a separate image stack which works quite 
> nicely.  The only problem I encounter is when viewing the data using 
> solid rendering only one channel is visible.  Is there a way to view 
> three image stacks at the same time using the solid rendering?
> Thanks,
> Tom

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110504/79611845/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: blend.jpg
Type: image/jpeg
Size: 35580 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110504/79611845/attachment.jpg>

More information about the Chimera-users mailing list