Geological Image Analysis Software - GIAS v1.0
Image Analysis Panel
The Image Analysis panel consists of the four graphical areas (area histogram, perimeter graphs, eccentricity histogram and an orientation rose diagram) and a text summary of the statistical properties of the image. It is only active if the input data is an image file (i.e. not an NN image or NN Centroid List). Note that previously processed data is stored in memory until it is overwritten.
The Image Analysis Panel uses the regionprops function within the MATLAB Image Processing toolbox calculates the following key properties of each object: area, centroid position, perimeter, eccentricity, orientation, equal-area circle equivalent diameter and a list of pixels positions within each vesicle.
The pixel list is used to determine which objects are in contact with the image edge and the equal area circle diameters are used to calculate object radii. The eccentricity and orientation are calculated by fitting an ellipse about the object. The angle between the major axis of the ellipse and the x-axis of the image defines the orientation
All graphs are for visualisation purposes only. You cannot export any of the figures directly (other than screenshot capture). The data to reproduce the graphs can be saved to a spreadsheet-readable text file. See Input Panel Help.
Area Histogram
The Area Histogram outputs the binned frequency of image object areas. The bin size defaults to 10 equally-spaced bins. All updates take place immediately.
However, depending on the distribution of the object areas, the user can change the bin size by selecting Custom and entering the required bin size (which are correctly scaled). The starting and ending size bins on the X axis can be chaged by selecting Custom and typing in the green boxes marked 'Min' and 'Max'. If you do not do this correctly, the Custom box will flash the word 'Value >' to remind you to enter the required values.
The Y axis can be displayed in either Linear or Logarithmic spacing. When the Log button is clicked, the bars of the histogram become single points. The Maximum frequency displayed on the Y axis can also be clipped.
To reset the values to Default, click on the Bin Size: Default button.. In the Y Axis (green) text box, type 'Max' to reset the frequency axis.
Perimeter Graphs
There are three graph options to choose from within the Perimeter option. The perimeter is the length about each object. Circular pixels will have the shortest possible perimeter for their area. Elongate, crennellated, agglomerated or convex shaped objects will have a perimeter that is longer than that of an circular object with equivalent area. All units are correctly scaled.

1. The user can choose to view a Histogram of the Perimeter lengths. This is a logarithmic x-axis graph and has no options to change the bin sizes or spacing.
2. A graph of Perim. vs. Equal-Area Circ. can be drawn which compares the perimeter of the pixels in each object with the expected perimeter of a circular object with equal area. A one-to-one ratio would suggest all the objects have a circular shape. A black dashed line shows this ratio - points deviating from this line indicate that the objects are not circular.
3. The Equal-Area Circ. Rad. plot gives a histogram of the radius of equivalent equal area circles. This can be used in addition to the other two graphs to decide the circularity of the objects.

Eccentricity Histogram
The eccentricity histogram outputs the binned frequency of object eccentricity. A circle has an eccentricity of 0, while an ellipse has an eccentricity greater than 0 and less strictly than 1. Eccentricity is deduced by fitting a major and minor axis to the each object. Note that elongate small objects will tend to have a eccentricity.
Orientation Rose Diagram
The orientation of each object is calculated as the angle offset of the major axis of the object counterclockwise from the x-axis of the input image. The maximum extent can be between +90 and -90 degrees. An ideally circular object has an orientation of 0 degrees.
The rose diagram is shown with an additional 180 degrees added on (to avoid the petals overlying the frequency numbers). Hence an orientation of 210 degrees is equivalent to +30 degrees. The angles and frequencies are correctly output to the CSV file.
Statistical Summary
The statistical outputs are shown in the top right corner of the Image Analysis tab. The Abundance metric shows the percentage ratio of black pixels (objects) to white pixels (background).
The other statistical properties are minimum, maximum, mean etc of the area, perimeter, eccentricity and orientation. These can be selected by clicking the appropriate button. All the data is output to the CSV file.