[Chimera-users] Volume segmentation question

Toby Starborg tobias.starborg at manchester.ac.uk
Tue Jun 5 10:22:52 PDT 2007

    Thank you for your quick reply.  I have indeed looked at using Amira 
to segment our data, but currently we do not have the resources to 
purchase it with all the necessary modules.

You have a good point about the possibility of removing too much data 
when trying to separate features by altering the threshold. My initial 
plan was to use the tools in a multi step process:  The first step would 
be to use a crude threshold that selects the features of interest plus 
extra voxels.  This step should hopefully eliminate many of the small 
particles that fill the tomograms (it could also be used to eliminate 
larger objects that you may not interested in, such as ribosomes when 
looking at intracellular structures). The idea was to use this crudely 
selected data set to find better thresholds with which to examine the 
features of interest.  This should be made easier because there would be 
fewer small (1-2 voxel) particles crowding the view. 
A problem I can foresee is that the pick surface pieces currently 
surrounds the voxels on all surfaces, ie it can turn voxels surrounding 
a stick-like structures into tubes.  To be able to use this method 
effectively the program would have to select the entire volume 
surrounded by the outer surface.

I accept that this is probably quite a rough and ready way of segmenting 
the data, but it strikes me as a quick method of removing unconnected 
data from the features of interest that is less prone to human error 
than using the volume eraser.

Thanks for the information on the bondzone.  This feature seems useful.  
A quick extra question.  Is it possible to increase the effective radius 
of colourzone?  I have a data set with a voxel size of 1 nm cubed, so 
the current maximum radius of 30 angstroms only selects a radius of 6 
voxels.  I can reset the effective voxel size, but this makes the images 
look odd due to the large magnifications needed.

Thanks again for all the 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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