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.
- 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.
- 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.
- 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.