FAQ
Frequently Asked Questions About FracLac for ImageJ
What is FracLac for?
When the details of design are as important as gross morphology.
It is for discovering patterns and trends in digital images using fractal and lacunarity analysis, along with several supplementary methods. It is a plugin for ImageJ.
What kinds of analysis can I do with FracLac?
See scan types.
Scanning Images
What types of image can I analyze with FracLac?
See images
What is the Scan button for?
This button uses the current scan settings to immediately scan the current image or stack or if an ROI is selected, creates a copy of the ROI, and scans it. See Scan Button.
How do I use the ParticleAnalyzer?
The ParticleAnalyzer is a tool built-in to ImageJ. Use it to automatically recognize and analyze particles in an image, such as cell nuclei.
To use it with FracLac, select the Sub Scan button and choose the "ANALYZER" option from the SCAN TYPE dropdown on the options panel that appears.
Scan ROI Manager
What is the ROIs button for?
The image shown here illustrates a scan using two oval ROIs and one rectangular ROI stored in the ROI Manager. The different colours show that the fractal dimension for each ROI was different. To generate colour-coded images, select the colour-coding option in the FracLac setup panel for the scan you are doing.
A Region of Interest (ROI) is an
area on an image that can be manually selected or
defined by coordinates stored in the
IJ ROI Manager.
Use this button on the FracLac panel
to scan a set of predefined ROIs in the Manager.
You can scan the set on a single slice image, stack, or
batch job of multiple images.
When you click the ROIs button, FracLac uses the
current scan settings
to scan the active image or stack, individually scanning
all of the ROIs currently in the Manager.
This is similar to a sub scan
but lets you specifically choose how to partition
your image and use overlapping ROIs if you choose.
You will also be asked if you want to use it if you
do a batch job.
Use it when you know the exact ROIs you want to scan, such as in an array.
If there are no ROIs in the ROI Manager, then a popup appears letting you know that it is empty and the scan is stopped.
How do I use the ROI Manager with FracLac?
Use ImageJ's built in
ROI Manager to automatically analyze several areas you select
ahead of time. See question above or an
explanation of what it does. Read on to find out how to start it.
First set up a scan, then
choose
Analyze >> Tools >> ROI Manager to
start the ROI Manager.
For each ROI you want
to analyze, choose a selection tool from the ImageJ menu
then select the area on the image and click add on the
ROI Manager. You can rename ROIs in the ROI Manager and
can also save or reload a set of ROIs if desired. Once your
set of ROIs is made or loaded, click the
ROIs button
on the FracLac panel.
How do I scan just the areas I select on an image?
To analyze an area on an image or stack that is currently open in ImageJ, select the scan type, then set up the options (when you select the scan type, this dialog appears to set the options), then use the selection tools on ImageJ to select a region of interest (ROI). Next, click the scan button on the FracLac panel.
See also ROIs Button
Batch Jobs
What is the Batch button for?
The Batch Button
Analyze directories of files automatically.
The Batch button (or SELECT FILES in older versions) is an alternative to the Scan button and the ROI Manager button.
- Use
this button to
- scan an image file stored on your hard drive without having to have it currently open.
- select multiple image files in one directory, and analyze them as a batch job during which you can select the option to save data and graphics results files automatically without viewing them on the screen.
What does the Close Windows Button on the FracLac Panel do?
This button closes without saving all open windows, including images, data, and graphs.
The Close Windows Button
This button is handy when many files have been generated and you do not want the data and graphics, but it should be used with caution. ALL open data and graphics files will automatically disappear into the void of nevermore.
Message Text
What is the bottom of the FracLac panel for?
At the bottom of the FracLac panel is a text area that indicates the type of scan that is selected, or else displays a message telling you to set one up. Use this to confirm settings in addition to scan type, such as image type, and background colour, before scanning.
File Extension
What does the "txt" button do?
It brings up a dialog box for the user to type a file extension into. The only two file extensions that are used are ".txt" and ".xls", and FracLac will change any input to one of those two extensions.
NOTE: Using the ".xls" extension does not change the basic formatting and is essentially the same as using the ".txt" extension; the choice is there for convenience and future development.
Help
How do I find help for FracLac?
- This help window is a major resource!
- Use the Online Help.
- Download the online Help archive from http://rsb.info.nih.gov/ij/plugins/ fraclac/fraclac.html
- or access it at http://rsbweb.nih.gov/ij/plugins/ fraclac/FLHelp/Introduction.htm
- or access it using the Help button on the FracLac panel.
- Try a tutorial from the online help.
- Check the Glossary in the online help. It has a lot of general and specific information about how to use FracLac in addition to diagrams and definitions for key terms.
- Check the citations page for examples of published research using FracLac.
- Report a bug, request a feature, or ask for assistance by email: akarpe01@postoffice.csu.edu.au
FracLac Help Button
If the Help File is in the IJ directory in a subdirectory called "plugins", in a file called "FLHelp", using the Help button will access that file.
Graphics, Data, and Raw Data Files
What are the results of an analysis?
The results are data files and graphics files that you select ahead of time from the options panel for the particular scan you are doing. You can see these on screen or select an option to save them automatically. The data and graphics are explained in detail on the relevant pages for the scan types
Refer to the scan type for details, because FracLac returns different types of information from each scan type. Moreover, within each scan type, it all depends on the particular settings. As an example of what to expect for a regular binary box count, if you select "Show Data", you will get, in addition to a main results table with the fractal dimension and various other parameters, files with the count of boxes and the mass in each each box at each box size.
How do I open data files?
Data files are UTF-8 encoded. They can be opened in text and word processors, ImageJ, or spreadsheets. To import a results file to a spreadsheet, select "UTF-8" encoding when asked for the character set or encoding type.
How do I colour-code images?
See colour-coding
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