FracLac for ImageJ

Audrey Karperien

Charles Sturt University 2000-2013

Software and Guide to Fractal and Lacunarity Analysis for FracLac 2013

FracLac for ImageJ
Overview
Sometimes the details of a design are more
important than gross morphology. FracLac for
ImageJ is for anyone who hopes to understand
this phenomenon through fractal analysis of
digital images. It presupposes that the curious
analyst has little background, and provides most
of what is required for one to become an
accomplished fractal analyst ready to discuss
the subtle, the beautiful, and the bizarre fractal
features of patterns sometimes imperceptible
to the eye yet mathematically detectable, and
perhaps more interesting, measurable, in digital
images.
FracLac for ImageJ is a toolset to help you
become such an analyst able to identify
and measure fractal features. It includes a
guide to fractals and fractal analysis, with
tutorials about basic and
advanced techniques, and
software to do fractal analysis.
Important topics covered
include technical issues and
interpreting results.
Whereas FracLac for ImageJ is
comprehensive and friendly
enough for the beginner, it also
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has advanced features for more complicated
analysis and more experienced readers.
The software is a free, open source plugin for
the free, open source imaging application
ImageJ. This free plugin is accompanied by free
detailed documentation (javadoc) with linked
and raw source code. Did I mention that it’s all
free? The advanced ImageJ user or researcher
can read the detailed implementations of the
math behind the program and its assumptions
in the source code and javadoc. Programmers,
moreover, can freely use or modify the code in
their own programs. Freely and for free!
How to Set Up and Use this
Document
There are several components to FracLac for
ImageJ This document is a shell that links to
content from an archive that includes all of the
components of FracLac for ImageJ. The archive
should be provided along with this document.
To use the resources, follow the steps below.
(Alternatively, you may wish to browse them
online, as explained in the next section,):
1) Depending on how you acquired the pdf
document you are now reading, the
components it links to will be embedded as
either an archive file in the pdf or a
supplementary archive (e.g., a zip file) available
from the download site.
2) If you have not already unzipped
the archive (e.g., you downloaded this
document separately from the archive),
unzip it to the same folder that this
document will reside in when you use it.
This is an important step so that
the links will work.
3) With the resources
stored in the same folder as
this document, you can
navigate to and fro amongst
the components using the
following links:
THE GUIDE plugin. How to set up the
This is the starting point and main plugin is described in the Guide
resource for learning about fractals above, but is also summarized
and fractal analysis. Here you will
below:
learn about such topics as what
fractals are and both basic and
1. Download and install
advanced fractal analysis concepts
ImageJ or ImageJ/Fiji for free from
and skills. The resources will help
the NIH’s ImageJ download site.
you learn and use a host of
methods with odd sounding names
2. Then, copy the
such as box counting,
Frac_Lac.jar file into the "plugins"
multifractality, lacunarity, sliding box lacunarity,
folder in ImageJ or ImageJ/Fiji, restart the
local fractal dimension, local connected fractal
app, and select FracLac from the Analysis
dimension, and mass-radius analysis, and some
menu.
complementary non-fractal morphometrics.
3. Click on the Help icon in the running plugin.
JAVADOC You can see the Help icon at the bottom
This component is the documentation that explains
right of the FracLac GUI in the picture.
the structure of the plugin’s code and details the
calculations. It is not as friendly as the guide but is a
gentle interface between you and the raw source
code. It explains how the code itself works. Refer to
it if you are a coder or you need the nitty gritty of
the calculations. There is much nit and equal grit in
there.

SOURCE CODE A Collaboration

This resource is a collection of text files known as
java classes. They are readable if you know the java
programming language or some other programming
language but are not usually useful to the
nonprogrammer. They can be used as the basis of a
new software project.
PLUGIN
This is the software, as a compiled “jar” file. To learn
how to install it, go to the installation page. The jar
file includes the source code as well as compiled
class files, and can be run in ImageJ or imported to a
software development environment such as
NetBeans or Eclipse. If you are not a coder, ignore
that last sentence.
Online Resources
As an alternative to using the links in the
previous section, you may wish to ensure you
are using the most up to date resources. You
can do this by browsing directly to the FracLac
site or by selecting help while running the
FracLac for ImageJ is alive and dynamic. The
software and guide are continually improving and
changing shape to meet the needs of the digital
image analyzing community.
Feedback and ideas for developing the software are
very welcome. All inputs will be considered! Free
support for FracLac for Image is available by email
through the online FracLac website.
The software and guide have been used in a variety
of fields to study phenomena as diverse as
agriculture, botany, dentistry, neuroscience,
pathology, geography, urban planning, and the far
away realms of the cosmos like the moon. If you are
curious about what some of those applications are,
the FLCitations page lists some 60 scientific papers in
which people have used FracLac to understand when
the details of design are as important as gross
morphology.
Enjoy!

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