Biology Reference
In-Depth Information
10. If you want to segment cells in an internal layer, you cannot use
this method for extracting the surface. Instead, you should use
the cutting surface, either the single plane of the Bezier surface.
Move the cutting surface to match the shape of the surface you
want to extract, and then use the mesh process “Mesh Cutting
Surface” to create the surface. To change the shape of the
Bezier surface: (a) draw the grid, (b) select the control points
by drawing rectangle around them by pressing the “Alt” key
and use the left mouse button, and (c) move them by pressing
“Shift” and “Alt,” left-click, and drag the control points.
11. If the surface is not visible, make sure the “Surface” check box
is ticked. It should appear in white. Show also the original
dataset (i.e., the main store) and check that the extracted sur-
face is close to the surface of the meristem on the image.
12. If some cells are too small and the adaptive subdivision erases
them, use the mesh process “Subdivide” in the “Structure”
folder.
13. You can hide the stack 1, or even reset it temporarily if you don't
have enough memory to load both images at the same time. All
we need to keep from the stack 1 is the segmented surface.
14. It is possible to project the subepidermal layer if the thickness
of the cells is constant enough. Set the minimum distance to a
value slightly above the thickness of the epidermal layer and
the maximum distance to a value slightly below the distance to
the third layer.
15. It is also possible to get the distribution of membrane markers.
In the heat map dialog box, you can select “Border signal,”
which is then the signal from the border to a distance smaller
than the “Border Size” parameter of the process. The opposite
is the “Interior signal,” which is the signal in the cell, but not
in the border. At last, you can compute a series of ratios, which
have been documented for endocytosis studies [
2
].
Acknowledgments
We gratefully acknowledge all those involved in the development
of the MorphoGraphX—Naomi Nakayama, Thierry Schuepbach,
Alain Weber, Anne-Lise Routier-Kierzkowska, and Micha Hersch.
We thank Daniel Kierzkowski for time series images and Cris
Kuhlemeier for discussions. This work was supported by SystemX.
ch, the Swiss National Science Foundation, EMBO Long-Term
Fellowship to S.R., and the University of Bern.
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