GRAPHICS

Colour Coded Local Connected Fractal Dimension Scan

Visualize Results and Set Options for Graphics Files

Use this panel to visualize results. The options on the GRAPHICS panel are available for most binary and grayscale scans.

Show Colour Coded Graphics After a Scan

colour code - Visualize variation over an image

Select this option on the GRAPHICS panel to colour code images according to the fractal dimension at each local area. You can colour code the distribution of the fractal dimension on images of single objects and images that are themselves collections of objects (e.g., arrays or particles).

This option is available for box counting, subscans, local connected fractal dimension scans, and mass vs distance scans.

Colour Coding on a Binary Image

This figure is a compilation of 5 scans of the image shown on the bottom right (i.e., an image of biological cells processed to binary). Each of the panels shows a colour-coded result enabled by selecting this option and doing a Sub Scan.

Colour-coding can also be selected for scans using the ROI Manager.

Sub Scan Using the ROI Manager Button

The figure shows a colour-coded result image generated in a standard box count scan using 3 ROIs stored in the ROI Manager; the image was generated by selecting the colour code option prior to scanning.

When this option is selected, coloured images are automatically generated after a scan.

Sub Scan Using Oval Samples

A simulated branching cell scanned using oval subsamples and colour coded to show local variation.

When this option is selected for single slice images analyzed on screen, a dialog appears letting you adjust the colours in real time. The images below, for instance, were made during a local connected fractal dimension scan, and the LUTs (sets of colours corresponding to fractal dimension ranges) were changed multiple times to highlight different features. See also subscans and multifractal analysis or refer to the online Help for more about colour coding and the distribution of fractal dimensions over images.

Retinal Vessels Colour Coded Using A Variety of LUTs

The panel shows one image colour-coded several times from one scan. The image shows retinal vessels; the scan was a local connected fractal dimension scan.

Help for how to set up colour options.

The real time editing option is not available for stacks or batch jobs so it is suggested to do preliminary runs on screen to establish values for these bulk jobs.

If many images are going to be made (e.g., with many slices in a stack or many ROIs), select the save results checkbox prior to scanning so they are stored in a file instead of displayed on the screen.

Diffusion Limited Aggregate Subscan

A diffusion limited aggregate scanned and colour coded as a regular array to show local variation in the fractal dimension. This image was scanned as a whole to get the fractal dimension for the image of around 1.7, then subscanned to investigate local variation.

Cells Automatically Partitioned from an Image Using ImageJ's Particle Analyzer
	This figure shows several biological cells that were automatically detected and colour coded according to the fractal dimension of each cell using a subscan with the Particle Analyzer.

Generate a Text Image for Local Dimension Scans

text image

Select this option on the GRAPHICS panel to make a text file of local dimensions that ImageJ can open, colour-coding each area as a single Dʙ.

Generate Regression Line Plots for Log-Log and Plain Data

regression - Graph regression lines for fractal dimensions

Select this option on the GRAPHICS panel to graph regression lines. When this option is selected, the program will generate saveable plots of regression data for the fractal dimension. These include graphs of ε vs count from box counting, as well as the log-log graphs of the same data.

Regression Line Graphs for log-log and non-log Plots of Size and Count

<html>Regression lines for
log-log plots and <br/>non-log plots of size and count

This option produces a potentially unwieldy number of on-screen graphs so it is recommended to select the option to save to a folder when this is selected.

Show Graphs of Lacunarity vs Calibre

lacunarity - Graph lacunarity vs Grid Calibre

Select this option on the GRAPHICS panel to generate graphs of lacunarity vs ε.

This option is to indicate whether or not to generate visuals. Lacunarity itself is always automatically calculated during box counting and sliding box lacunarity scans, and results are reported in the data files, regardless of whether or not this checkbox is selected.

The data from which lacunarity is calculated will be different in a multifractal scan compared to a regular box counting scan because the settings for grid sizes, sampling grid orientation, etc. are generally different.

Set the Scale for Lacunarity Graphs

same scale - Use one scale to compare lacunarity graphs

Select this option on the GRAPHICS panel to use one scale for all lacunarity graphs. When this option is selected, the program will generate all lacunarity graphs in a job using one scale so that they can be visually compared; otherwise the limits of the axes will be determined based on the individual data for each scan.

This option is disabled if the option to show lacunarity graphs is not selected.

Generate Histograms of the Fractal Dimension

distributions - See how the fractal dimension was distributed on an image

Select this check box on the GRAPHICS panel to generate histograms that show the distribution of fractal dimensions over an image. Use these along with colour coded graphics and data files.

This option is available for Sub Scans and Local Connected Fractal Dimension Scans.

Histograms of Distribution of Fractal Dimensions

$Histogram of distribution of fractal dimensions$

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