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done by application of some test system (composed of points, lines,
quarter-circles, cycloids, etc.) and counting the intersections of the
structure under study and parts of a test system (e.g., refs. [ 2 , 3 ]);
for introduction to stereology see also C. V. Howard's web pages
( http://www.liv.ac.uk/fetoxpath/quantoxpath/stereol.htm ).
Stereological methods along with uniform random sampling can be
very effi ciently used to get unbiased estimations of quantitative ana-
tomical parameters of plant organs. For more details on principles
of stereological method application see the source studies [ 5 - 9 ].
In this chapter, several examples of basic procedures for quan-
tifi cation of plant structures are presented. We focused on param-
eters which can be quantifi ed from 2D images: length, surface area
in 2D, particle density of particles laying in one plain, and analysis
of epidermal cell shape.
The very important rules for obtaining reproducible results of
image analysis are the following: (1) object sampling should be done
on the base of uniform random sampling to achieve unbiased estima-
tion, (2) right calibration has to be set to obtain results in right units,
(3) proper statistical rules and methods have to be applied during
results processing and interpretation, and (4) all used methods have
to be thoroughly described with enough details to enable reproduc-
tion or comparison of obtained results by other researchers.
2
Materials
There are many commercial image analysis programs, which can be
successfully used for the following tasks. All examples in this chap-
ter are described on the public domain program ImageJ [ 10 ]. The
ImageJ program can be downloaded from http://imagej.nih.gov/
ij/ , which also provides a detailed installation manual, documenta-
tion, user manual, and many plug-in modules for various tasks. The
program is based on Java and runs on Windows, Mac OS, Mac OS
X, and Linux. Its source code is freely available and anyone can
program further plug-ins to be added into the program ( see Notes
4 and 5 ). The program window consists of three lines: Menu
Commands (“Menu” in the subsequent text), Toolbar (“Tools” in
the subsequent text), and Status and Progress Bar (Fig. 1 ).
Fig. 1 ImageJ window with menu bars: upper bar Menu Commands (“Menu” in the text), middle Toolbar
(“Tools” in the text), and lower Status and Progress Bar
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