Biology Reference
In-Depth Information
Fig. 3
(
a
) Surface with projected signal and seeds. Note the line of purple seeds all around that will mark the
outside of the area of interest. (
b
) Result of the fi rst (coarse) segmentation step. (
c
) Segmentation error. (
d
)
Erasing the labels and redrawing close to the cell wall. (
e
) Corrected segmentation. (
f
) Projected image with
very small triangles. The voxels (0.5
m) can be seen in the projection. (
g
) Smoothed projection. (
h
) Different
sizes of triangles (in
yellow
) depending on their position with respect to the cells. The boundary between cells
is shown as a
blue line
. (
i
) High-quality segmentation
μ
the area of a voxel, and the “Border Dist” should be between
the max size of a triangle and under half the size of the smallest
cell. If a triangle is not entirely in the border, it won't get sub-
divided (
see
Note 12
); however, if the “Border Dist” value is
too large, it will clear the small cells entirely. When experi-
menting with parameters here, be sure to save your initial seg-
mentation to a fi le so that it can be restored if labels get
accidentally cleared.
8. Use the mesh process “Project Signal” in the “Signal” folder,
followed by “Smooth Mesh Signal.” This will re-project and
smooth the signal, which should make the walls look smoother
with each iteration (Fig.
3g
). Next, run the “Segment Mesh”
process to re-segment the newly subdivided surface.
9. Repeat
steps 6
and
7
until the cells walls are suffi ciently
smooth or the number of vertices in the mesh stops increasing
(visible in the status bar at the bottom of the MorphoGraphX
window). When the triangles get smaller than the voxels, you
will see squarish blocks of signal on the surface when you
zoom in (Fig.
3f
). At this point further subdivision will not
increase the quality of the segmentation.
10. Use the mesh processes “Fix Corners,” followed by “Segment
Mesh” in the “Segmentation” folder. This will subdivide
the corners between cells that were not labelled by the seg-
mentation process and relabel them. Iterate this step until the
“Fix Corners” process reports that no vertex has been deleted
and that no triangle has been subdivided (visible in the status
bar at the bottom).
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