Software for the Image Analysis of Cheese

Microstructure from SEM Imagery

Gaetano Impoco
impoco @ dmi.unict.it
September 12, 2007

Contents

This software is intended for the analysis of SEM 1 imagery of cheese microstructure. It might be also used in connection with different acquisition
technologies or for different applications where porous materials are involved.
However, being tailored to a specific application, you cannot be sure it will
be of any use in your application. Applicability of this software should be
evaluated for every specific application.
This software is in the form of a plug-in for ImageJ [3]. ImageJ is a
widely used Open Source software in scientific communities employing Image
Analysis and is released under the GPL license [1]. Figure 1 shows a snapshot
of ImageJ and the plug-in for the analysis of cheese SEM imagery. The plugin encompasses two commands:
BinariseSEM
ComputeStats.
BinariseSEM segments 2 the input image into holes and structure i.e.,
in areas that are interpreted as pores or as protein matrix. It is useful to
remark that:
1

Scanning Electron Microscope.

To partition an image into a number of classes, using a coherence criterion within each
class.
2

Figure 1: A snapshot of the ImageJ software and the plug-in for Image
Analysis.

 Holes and structure that are not imaged (i.e., acquired by the microscope) cannot be processed by no Image Processing software, simply
because they are not visible.
Pores with diameter of one pixel o less are discarded since they are
treated as acquisition noise.
The definition of pore used here does not necessarily coincide with the
informal definition nor with the expectations of the user. In particular,
here a pore is defined as a set of contiguous pixels whose intensity
values are coherent. The coherency function derives from the sequence
of operations used to enhance the input image before thresholding 3 )
The command ComputeStats employs the output of the previous application BinariseSEM to collect image statistics about the distribution of pores,
such as: number of pores, perimeter and area, shape descriptors, orientation,
and so on.
It is assumed that input images are achromatic (i.e., greylevel) and with
a bitdepth of 8-16 bit/pixel.

Installation

The installation procedure of ImageJ plug-ins is quite simple. Just extract

the content of the downloaded compressed file into the directory [ImageJbaseDir]/ plugins/ where [ImageJbaseDir] is the ImageJ installation directory, and run ImageJ.

The Plug-in

The SEM analysis plug-in has two commands that must be used in the correct sequence. ComputeStats takes a binary image as input, where it is
assumed that white pixels belong to holes and black pixels represent structure. BinariseSEM outputs this kind of images, given a greylevel SEM
image.
3

Image Processing operation used to segment the image using a threshold value. This
term is mainly used for binary segmentation (i.e., with two classes only).

We chose to break the plug-in into two commands in order to allow easy
substitution of BinariseSEM with another binarisation software giving the
same output (for example, a simple global thresholding). A more detailed
presentation of the two commands follows. For a description of the algorithms
used the reader is referred to [2].

3.1

BinariseSEM

This command segments the input image into pores and structure, where a
pore is defined as a patch of contiguous pixels with similar intensity values.
A discontinuity in the pixel intensity is regarded as a discontinuity in the
structure of the material. This might be not always true, due to noise and
reflection effects caused by the acquisition device.
As shown in Figure 3, after opening an image e selecting the BinariseSEM command in the menu, a dialog window is shown. Two options are
given: Bandpass Filter e Fill Inner Holes. It is asked to the user to guide
the segmentation mechanism since these two parameters are strongly dependent on the application and on the domain knowledge of the user, and their
values cannot be automatically guessed for every application. In particular,
the second option lets the user choose wether the holes must be filled or not
after thresholding. Hence, it should be turned on only if the user knows that
there cannot be any structure inside a hole.
The first option is used to correct possible illumination gradient effects
due to the acquisition system. When activated, a filter is used to correct for
intensity gradients but, at the same time, the image quality is reduced so
that the quality of the output could reduced as well. Hence, care should be
taken when using this option. Before using the software for massive analysis,
we recommend to run this command twice for each image using this two
options alternately in order to get the feeling of the result.
After selecting the desired options the command is run. A sequence of
processing operations are executed to enhance the quality of the input image
and to make it more amenable for thresholding [2]. When the processing ends
a window is shown to help the user choosing the best threshold value for the
application (Figure 3(a)). The plug-in automatically computes a threshold
value that is suggested to the user. Ino most cases, this value gives a good
thresholding. However, an automatic procedure cannot give optimal results
for all applications and has no knowledge about the domain of application.
Hence, the thresholding procedure must be assisted by the user. When the
4

(a)

(b)

Figure 2: Options of the BinariseSEM command.

5

(a) Thresholding of the processed image.

(b) Binary output image.

Figure 3: Thresholding.
6

threshold value has been chosen the output will appear as in Figure 3(b).

3.2

ComputeStats

This command collects various statistics about the holes extracted using the
BinariseSEM and shows them using histograms and rose plots. Figure 4
shows the options of this command. The most important is the magnification
factor of the microscope, expressed in microns. The other options refer to
the statistics to evaluate and show. Figure 5 reports an example of the
output of this command. Histograms are shown reporting the distribution of
several measures and of the value of some shape descriptors (see [2] for a more
detailed description). All the distributions are summarised by histograms.
Directionality can be also shown using an angle diagram (rose plot). One
such diagram is shown on the bottom right of Figure 5. Notice that the
statistics about directionality report a predominant orientation of the pores
approximately around 45 with respect to the x-axis (see the rose plot and
the histogram on its left).

References
[1] Free Software Foundation. GNU General Puplic License. Web site: http:
//www.gnu.org/licenses/licenses.html#GPL.
[2] G. Impoco, S. Carrato, M. Caccamo, L. Tuminello, and G. Licitra.
Quantitative analysis of cheese microstructure using sem imagery. In
SIMAI 2006. Minisymposium on Image Analysis Methods for Industrial
Application, 2006.
[3] Research Services Branch NIMH & NINDS. ImageJ - Image processing
and analysis in Java. Web site: http://rsb.info.nih.gov/ij/.

(a)

(b)

Figure 4: Options of the command ComputeStats.

(a)

(b)

Figure 5: Statistics computed.

9