Geological Image
Analysis Software - GIAS v1.0
Input Panel
The
input panel consists of the four main areas - the display axis, Input
Parameters, Detection Parameters and the Outputs. These can be used to
input data and control the parameters used when processing the image or
NN Centroid List. Results can be output and saved to a separate text
file for graphing and analysis with other packages.

Display
Axes
The
Display Axis
initially shows the GIAS logo. When a file or image is loaded,
it is
displayed in this area to allow the user to ensure they have the
correct file. No image processing takes place within the file, so the
input image is not altered in any way.
Inputs
- The
input panel area consists of four buttons and three tick boxes. The
user can load in three
types
of data using the Load
Image button
- An 8-bit gray level image
(e.g. vesicles image). Note the larger the image, the longer the
software will take to run (and the more memory required to do so). If
an image is loaded, the Image Analysis panel and the Nearest Neighbor
panels will be updated. The application assumes by default that an
image will be loaded. Click on Load
Image to open a file browsing panel to find the required
file. If the file does not have white background with dark vesicles,
the user can Invert
Input Image polarity, to reverse the black/white pixel
settings. The image to be processed appears in the Display Axis. The following formats are recommended: *.tif, *.jpg
- An image with white pixels
indicating the centroid positions of features to be analysed. Choose
the NN Input Image
tick-box before clicking on Load Image to select
this type of input. Only the Nearest Neighbor panel will be active. The
image to be processed appears in the Display Axis. (Note due to the
resolution and scaling of the input image for display purposes, the
white pixels might not be visible)
- A two column (space or
tab-delimited) list of the x- and y- positions of feature centroids. Choose
the NN Centroid List
tick-box before
clicking on Load Image
to select this type of input..Only
the Nearest Neighbor panel will be active. A two-pixel wide
'image' will appear in the Display Axis to show that the data has been
loaded.
- Once the Image or List has been
input, click on Process
>> to begin analysis of the data.
- When the graphs have been drawn,
the results can be saved to Tab-Delimited files, whose names begin with
the string entered in the Output
text box, using Save
Results.
- Finally, to exit the application,
use the Quit
button.
Detection
Parameters
The
parameters associated with the image to be processed can be altered to
remove large or small pixel objects for graphing or analysis reasons.
The Process
>> button must be clicked each time one of
these parameters is changed, to update the graphs and output data.
- The Minimum
Object Area text defines objects with area size
smaller than this number ( in
pixels) which are to be ignored. For example, objects
which have an area of 1 pixel may be spurious noise pixels,
while it might be desirable to have objects with at least 3x3
(=9) pixels in order to define a vesicle. Note that the Minimum Object
Area is defined in
pixels in order to remove any confusion related to the
actual pixel units.
- The Maximum
Object Area text defines objects with area size larger
than this number ( in
pixels) which are to be ignored. Often, an image may have
a few very large objects, which dominate the statistical analysis. By
removing the larger objects, data displayed histograms and other graphs
may become more manageable. Setting the slidebar to 'Max' includes all
of the objects in the analysis.
- The Black/White
Threshold Level allows
the user to define the black/white cutoff threshold in Digital Number
units (0-255). The default value is 250, meaning that pixels with
values above this number are set to white, while pixels with a value
less than this are set to black. This option is present because the
input image is converted from an 8-bit gray level image to a
binary image for processing.
- Normalised
Poisson Area: This option allows the user to define the
minimum area resolution for use in the Normalised Poisson Model (see
the Nearest Neighbor Panel Help). Pixel Units are used for the distance..
Remember, the Process >>
must be clicked to implement any adjusted detection parameters.
Outputs
The
Output area controls the name of the output files, the units of the
input image or list of data and whether the pixels touching the
boundary are used in the process for Nearest Neighbor and Image Analysis.
- The user can change the filename
of the output files by entering text into the green text box (and
pressing the Enter/Return key when finished). The output consists of
one or two files depending on the input.
- If the user inputs an image which is processed and
outputs data
to the Image Analysis and Nearest Neighbor panels, then two output
files are created - one for each panel.
- If the user inputs an NN image or NN Centroid List, then
only one
output file is created, giving the Nearest Neighbor outputs.
- The Pixel
Size can be defined in units of microns, millimetres or
metres. Type the pixel size (i.e. one dimension) into the green text
box and select the appropriate unit. If only the pixel area is known,
then this can be entered, though the pixel shape will be assumed to be
approximately square for processing purposes.
- Ignore
Boundary Objects: For the purposes of Image and
Nearest Neighbor analysis, objects that touch the boundaries
should not be used, as their maximum properties are unknown
(e.g. we see only a minimum extent). These objects are ignored by
default. To include them in the Image analysis, uncheck the tick-box.
They will still be ignored in the Nearest Neighbor analysis, as they
may have a nearest neighbor just beyond the boundary of the image.
The File Outputs to the the CSV file can be imported directly into an
EXCEL or OpenOffice Calc spreadsheet for additional graphing or
analysis. All the calculated values and statistics from the application
are output to this files. See the example output files for further
details.