FracLac for ImageJ

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Nov 15, 2013 - Refer to it if you are a coder or you need the ... If you are not a coder, ignore that last ... support for FRACLAC FOR IMAGE is available by email.
FRACLAC FOR IMAGEJ Audrey Karperien Charles Sturt University 2000-2013 Software and Guide to Fractal and Lacunarity Analysis for FracLac 2013

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!

There are several components to FRACLAC FOR IMAGEJ. This document is a shell that links to the other components (see next page), which are assumed to be in a folder in the same directory as this pdf. To set up the archive, follow the steps below.

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 has advanced features for more complicated analysis and more experienced readers.

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1) Get the archive. Depending on how you acquired the pdf document you are now reading, the archive will be either embedded in the pdf itself or available for download from the site you downloaded the pdf from. 2) Unzip the archive to the folder that this document is in. Otherwise the links will not work. Remember the old real estate adage, location, location, location! 3) Navigate to and fro amongst the components using the links.

Go to the starting point and main resource for learning about fractals and fractal analysis. Here you will learn about such topics as what fractals are and basic to advanced fractal analysis concepts and skills. The resources will help you learn and use a host of methods with odd sounding names such as  box counting  multifractal analysis  lacunarity sliding box lacunarity local fractal dimension local connected fractal dimension  mass-radius analysis and complementary non-fractal morphometrics.

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 plugin. How to set up the plugin is described in the Guide above, but is also summarized below: 1. Download and install ImageJ or ImageJ/Fiji for free from the NIH’s ImageJ download site. 2. Then, copy the Frac_Lac.jar file into the "plugins" folder in ImageJ or ImageJ/Fiji, restart the app, and select FracLac from the Analysis menu. 3. Click on the Help icon in the running plugin. You can see the Help icon at the bottom right of the FracLac GUI in the picture.

Go to the documentation explaining the structure of the plugin’s code and details about the calculations. It is not as friendly as the guide but is a gentle interface between you and the raw source code. 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. Go to 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. Go to the folder holding 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.

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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 components of FRACLAC FOR IMAGEJ 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 it to understand when the details of design are as important as gross morphology. Enjoy!