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

1. 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
2. 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)
3. 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.

1. 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.
2. 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.
3. 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.
4. 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.

1. 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.

2. 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.
3. 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.