[Chimera-users] zone tool and volume rendering

Thomas Goddard goddard at cgl.ucsf.edu
Tue Jan 30 09:26:36 PST 2007

Hi Jeff,

  I'll tell you my experience looking at a tomogram (2048 x 2048 x 76) 
of an immune synapse for a demonstration I gave last month at a cell 
tomography workshop.  The file (mrc) is too large to conveninently 
display at full resolution.  So I made binned versions 2x and 4x smaller 
along each axis (file size 8x or 64x smaller).  Then I used the 
precomputed subsamples feature I described before.  For some added 
convenience I then saved the map to a NetCDF file using Chimera because 
this saves the full matrix and binned versions in a single file (new in 
Chimera 1.2318).  I use the volume dialog data display options to 
"Adjust step size to show at most 1 Mvoxels", or however many million 
voxels my computer can handle without getting too slow.  Then I use the 
full view of the data to find regions I'm interested in, then use the 
subregion selection feature and Crop button to look at a smaller piece 
and the step size automatically is reduced.  If I choose a small region 
I get full resolution.  When doing this you have to keep in mind that 
once you manually change the step size at the top of the volume dialog 
it turns off the automatic step size adjustment.  So I try to avoid 
that.  Of course I also use the volume planes tool.

  I think you know all this and probably are using Chimera to the best 
of its current capabilities.  You want to push it to use better 
compression (like resampling to have better aligned boxes) so you can 
see more data at full resolution.  We don't have that yet.  It is not 
hard to envision much fancier compression implementations that improve 
performance.  Chandra Bajaj at U. Texas is very interested in this and 
may have software you can use.  You might want to try his VolumeRover 
program.  The Chimera EM capabilities were developed for single particle 
reconstructions.  We have done little in Chimera to support work with EM 
tomograms which are very different in size and content (non-axis aligned 
structures, membranes, ...).  We plan to develop tomogram capabilities 
and my volume planes tool created last month is a tiny step.  But it 
will take years to implement the obvious stuff we can think of now.  
Your comments are helpful in guiding the priorities.

  I don't understand why you are "jotting down displacements" when 
saving subregions.  Chimera puts that info into the MRC header.  So why 
do you need to write it down?


 Jeff  wrote:
> thanks Tom,
> with regards to the rotation/resampling, I was thinking mainly in 
> terms of visualizing large #'s of filaments and membrane, which in 
> themselves only constitute a small fraction of the actual volume they 
> traverse. even if re-sampling were done by cubic interpolation onto a 
> the same dimensioned grid, in some cases the loss in resolution would 
> be acceptable (definitely would be acceptable for some of my current 
> needs). i have problems with visualizing my whole maps unbinned but 
> was thinking that the savings such an approach would represent could 
> allow me to do that. for instance, this is already a problem for me 
> with trying to volume render a slab of membrane, which I think might 
> contain interesting features but I can't get the whole thing to go 
> unbinned; if it were rotated into the minimal enclosing volume, 
> interpolation artifacts or otherwise, my feeling was that I might 
> overcome that (there are also a bunch of filaments attached to the 
> membrane, and running underneath the membrane, so it is a real 
> difficulty for me to go back and forth between cutting out subvolumes 
> and binning them to be manageable, segment out filaments, or membrane, 
> etc, then try to put all the segmented items back into the same volume 
> and have a look-see).
> the volume planes tool has proven very helpful in segmenting out the 
> membranes, though. to get at the filaments that are attached to the 
> membrane, I was zoning out a region around the membrane (placed a 
> bunch of markers on the membrane using volume planes tool) about 400 A 
> in radius, but this proved difficult to render in the entire tomogram 
> b/c the zoned membrane still encompassed most of the original volume, 
> etc. so I was back to having to cut regions out of that segmented 
> membrane map to look further. (thus necessitating me jotting down the 
> displacements of each subregion, etc.)
> -jeff

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