Find locations of dendritic shafts in the mesh generating code

[dhermes]

/cc @subroutines

[dhermes]

@subroutines The constants are defined here: https://github.com/subroutines/djhbrm/blob/d58b9581e52f582656ae2aa9c993d6b9e94664be/dolfin_code/full_dendrite_mesh.py#L15

This is the file where the mesh file is created.

The four vertical dendritic shafts are identical except for a horizontal shift. The first one is centered around (x, y) = (0, 0). Each after is shifted by 2.0 in the x-direction and none in the y-direction so the other centers are (x, y) = (2, 0), (x, y) = (4, 0) and (x, y) = (6, 0).

Each shaft is composed of a cylinder, then a truncated cone pointing down and then a truncated cone point up. The truncated cones are defined by their centers and by the radii of their upper and lower circles.

Each of these lower cylinders has radius 0.1 and goes from a height of -0.1 to 1.0 - 3 * 0.16 = 0.52. Then the lower cone has a lower radius of 0.1 (to match the cylinder) and continues to an upper radius of 0.3 at a height of 1.0 - 0.16 = 0.84. Finally, the upper cone has a lower radius of 0.3 (again to stack on top of the lower cone) and continues to an upper radius of 0.2 at a height of 1.0.

In order to make dolfin behave, all these were scaled up by a factor of 50.

[dhermes]

Assigning to you, feel free to close it out if this resolves what we need.

[bradmonk]

So the circle on top of the upper cone (the synapse: https://www.youtube.com/watch?v=9ipFHrxqLWc) has a radius of .2*50 = 10? This is advantageous, because the radius I've been using to model actin at the synapse is 10.

[dhermes]

The model radius is still 0.2. Yes, effectively, the radius is 10 but it's really just a matter of how you look at it.