[Chimera-users] Volume segmentation question
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
Thank you for your help.
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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