[Chimera-users] Automate Segmetation

Soumya Govinda Remesh sgremesh at lbl.gov
Tue Oct 10 17:04:53 PDT 2017

Hello Chimera Developers,

 There is this repeated procedure that I have to do to get a Segmented map
from my soft x-ray tomography maps. Here is what I want do:

1. open  *mrc

put the map to Level 0.011

2. *vop  gaussian  #0 sd 0.005*

put Gaussian to 0.011

3. Go to: Tools --> Volume Data --> Segment Map

Segment the gaussian map

Smoothing step: 1

Step size: 500 voxels

Keep only regions at lease: 100 voxels

Save segments as an .mrc file

Go to: File (Segment Map) --> Save all regions to .mrc

Set Segment map to 0.011

4. Type:
*vop subtract #3 #0*

#3 Corresponds with ID# of the segmented .mrc file

#0 Corresponds with ID# of the original file

5. *sop split #0 *

#0 Corresponds with ID# of the original file

   - Splits surface into disconnected parts

The steps in *bold *are in command line. Is there anyway to have everything
in a script format? Setting the levels, opening segmentation and setting
values to specific Voxel values every time is quite time consuming. I would
appreciate your help. Thanks

Soumya Govinda Remesh, Ph.D.
Postdoctoral Fellow at Advanced Light Source
SIBYLS group: http://sibyls.als.lbl.gov/
Lawrence Berkeley National Laboratory

1 Cyclotron Road   MS 6R2100
Berkeley, CA 94720
(phone) 510-495-8179
(cell) 804-402-8730

sgremesh at lbl.gov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20171010/23b344be/attachment.html>

More information about the Chimera-users mailing list