[Chimera-users] Volume segmentation question

Toby Starborg tobias.starborg at manchester.ac.uk
Mon Jun 4 05:21:22 PDT 2007

Dear Chimera users.

    I am new to using chimera, so this question may seem a bit simplistic.
I'm trying to use Chimera to examine EM tomographs of fairly busy data 
sets.  I'd like to be able to divide the data into separate features so 
that I can better understand which parts are noise and which are 
structural (segmentation).  So far I have found the "Pick Surface 
Pieces" tool is very useful for colouring the surface of features of 
interest.  I have also found it useful to colour some surfaces with 0 
opacity to remove items that are in the way, but I would prefer to do 
this in a more permanent fashion sot that I can return to a data set and 
quickly compare structures. 
I have also tried using "Volume Path Tracker" with "Color Zone" and 
"Split Map by Color" (after adjusting the voxel size to angstroms rather 
than nm to give a reasonable volume segmentation). 

My question is would it be possible to alter "Pick Surface Pieces" so 
that it colours (or tags in some way) all of the voxels within the 
chosen mesh, so that it would then be possible to split the map into 
separate compartments that could be saved and examined separately?  This 
would also offer the ability to use different threshold levels to 
examine different features.

I realise that this is more of a wish list than a trouble shooting 
question, but I'd also appreciate any input from more experienced 
Chimera/tomography users.

Thank you for your help.

Toby S

Dr T Starborg
FLS, University of Manchester
Michael Smith Building, Rumford Street, Manchester,M13 9PL. UK
tel:+44(0)161 275 1557 fax +44(0)161 275 1505 

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