Biology Reference
In-Depth Information
Chapter 10
Quantifying Cell Shape and Gene Expression in the Shoot
Apical Meristem Using MorphoGraphX
Pierre Barbier de Reuille , Sarah Robinson , and Richard S. Smith
Abstract
Confocal microscopy is a technique widely used to live-image plant tissue. Cells can be visualized by using
fl uorescent probes that mark the cell wall or plasma membrane. This enables the confocal microscope to
be used as a 3D scanner with submicron precision. Here we present a protocol using the 3D image pro-
cessing software MorphoGraphX (
http://www.MorphoGraphX.org
)
to extract the surface geometry and
cell shapes in the shoot apex. By segmenting cells over consecutive time points, precise growth maps of the
shoot apex can be produced. It is also possible to tag a protein of interest with a fl uorescent marker and
quantify protein expression at the cellular level.
Key words
Shoot apex, Confocal microscopy, Image analysis, Segmentation, Watershed, Shape analy-
sis, Expression pattern, 3D visualization
1
Introduction
MorphoGraphX is an open-source application designed for the
visualization and processing of data in 3D either as volumes (i.e.,
3D images) or as surfaces. In this chapter, we will present the pro-
tocol used to extract information from the shoot apical meristem of
the tomato or
Arabidopsis thaliana
, as published previously [
1
,
2
].
Also provided in the notes are variants of this protocol for use with
other tissues, such as the Arabidopsis root [
3
].
MorphoGraphX can manipulate two kinds of data:
stacks
(3D
volumetric images) and
meshes
(triangulated surfaces).
A
stack
corresponds to a specimen for a given time point and
contains two images, called
stores
: the main store and the work store.
When processing images, MorphoGraphX can use either store as
the input but always writes to the work store. This allows the use of
the main store as a checkpoint while optimizing parameters.
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