[Insight-users] Fitting a 2D mesh model to a 2D image?

[Zachary Pincus]

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Hello,

I've run across the need to place some sort of coordinate system on 
images of bent bacteria for the purposes of making measurements of 
protein localizations that can be compared across populations.

My first-pass idea was to make a 2D grid from an ITK mesh, and then use 
some of the FEM model-based segmentation/registration methods to fit 
the grid to the bacterial image. (See attached image for a vague idea 
of what I'm talking about.)

However, from reading the documentation for the DeformableMesh3D 
filter, I'm not sure if it will work off the shelf. It seems (and I am 
likely to be wrong) that this filter is more designed to work with the 
output of something like a marching cubes algorithm (or in my case, 
marching squares) that defines only the edge of the structure (that is, 
some manifold surface embedded in a higher-dimension space, like a 2D 
surface of a 3D object, or in my case, a 1D perimeter of a 2D object). 
Do the DeformableMesh3D methods work with dense meshes of the sort I'm 
proposing in the image below?

It almost seems like I need some hybrid between the FEM deformable 
image registration methods and the model based segmentation methods. If 
the DeformableMesh3D methods won't work, are there other things that I 
could try off-the-shelf from ITK? If not, does anyone have any 
suggestions as to which classes I might try to build off of?

Thanks for any input at all,

Zach Pincus

Department of Biochemistry and Program in Biomedical Informatics
Stanford University School of Medicine


Attached: Figure 0, in which my imagined inputs and outputs are 
illustrated in a most mediocre manner.

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