[Insight-users] Morphogenesis

[Luis Ibanez]

Hi Daniel,

Instead of the Morphogenesis application,
you may want to use the most recent example:

       CellularSegmentation

It has a simplified interface and use just
bacteria that grows and replicates as long
as the intensity of the image is inside the
range that you select on the GUI.

Make sure that you first click in the image
in a pixel that is inside that range. This
click operation will place an egg cell in
the image, and from it the bacterial
replication should start.

Since you are interested in generating 3D
Meshes, you will need to modify this
application a bit.

Note that the CellularAggregates use over-
connected meshes that needs to be simplified
in order to get a partition Mesh.

However, the bacterial growth is a good
mechanism for filling in a volume with a
relatively uniform distribution of cells.

In the 2D case we use the vtkDelaunay filter,
you may want to do something similar in a
3D version.


Please let us know if you have further questions,


   Thanks


     Luis


--------------------------
Einstein, Daniel R wrote:
> Hello,
> 
> I am intrigued by the morphogenesis example and would like to modify it 
> to generate CFD compatible meshes. I noted that there have been some 
> email strings related to volume mesh generation and the application. 
> Anyone know what became of those attempts?
> 
> Plus, I have a couple of questions:
> 
> 1) I am not sure that everything is installed properly. It builds and 
> executes but the gradient eating bacteria do not seem to replicate. I 
> have placed them in the  substrate and given them a threshold (by 
> modifying the .dat files), but they do not seem to grow. I want to 
> figure out if the build is correct. Can someone tell me what image was 
> used in the demo? I would like to try to replicate exactly with the same 
> settings so that I can figure out what is going on.
> 
> 2) What is the relationship between the CellularSegmentation application 
> and the Morphogenesis application? Anything?
> 
> 3) At no point do I get tetrahedra as are pictured in the demo movie. 
> Was this created somewhere else? The cell viewer in the Morphogenesis 
> application seems not to do anything. Might this be an indication that 
> something is amiss?
> 
> 
> Any and all help is greatly appreciated.
> 
> Dan
> 
> 
> Daniel R Einstein, PhD
> Biological Monitoring and Modeling
> Pacific Northwest National Laboratory
> P.O. Box 999; MSIN P7-59
> Richland, WA 99352
> Tel: 509/ 376-2924
> Fax: 509/376-9064
> _daniel.einstein at pnl.gov_ <mailto:daniel.einstein at pnl.gov>
> 
> 
> 
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