Biology Reference
In-Depth Information
Fig. 2
(
a
) Clipped view of the meristem after the “Edge Detect” process. The work store is shown in
red
and
the main store in
green
. Where there is signal from both stores, the color visible is
yellow
. The
red
should not
be visible above the
green
of the main store. (
b
) Surface of the meristem with the bottom and the sides
selected, ready for deletion
5. Use the mesh process “Marching Cubes Surface” in the
“Creation” folder to extract the surface [
8
]. The cube size
should be around half the size of a cell, so as to capture the shape
of the meristem but not surface noise (
see
Notes 10
and
11
).
6. To reduce the number of vertices required, the bottom of the
mesh can be removed. First visualize the triangle mesh by tick-
ing the “Mesh” checkbox and un-ticking the “Surface” check-
box of the stack 1.
7. With the mouse move the camera to view the meristem from
the side. Once the view is close to an axis, you can double-click
the left button to align it to the axis. This will make it easier to
select the bottom row of vertices. Using the “Select points in
mesh” tool, select the bottom and the sides of the mesh
(Fig.
2b
). The vertices should turn red once selected. Press the
“Delete” key to remove the selected vertices. Remove all parts
of the mesh you do not need/want.
8. Smooth and refi ne the mesh using the mesh processes
“Smooth” and “Subdivide” in the “Structure” folder. Apply
them both until you get about 5-6 points across each cell. Be
careful not to run this too many times, as the vertex count will
roughly quadruple each time. You may want to smooth several
times when you fi rst start to remove small bumps in the
surface.
9. Un-tick the mesh checkbox and tick the surface and main
check boxes in the stack 1 to show both the surface of the
mesh and the original, cleaned image.
10. Use the mesh process “Project Signal” in the “Signal” folder.
The parameters indicate how deep into the stack the signal is
taken from. Be sure that the main store is selected and that the
work store is not. Otherwise you will project the uniform sig-
nal from the fi lled-in stack. The minimum distance should be
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