• Installation
• Getting images for analysis
• Image preparation
  
• Image analysis
• Results

Installation

For running the aplication we recommend computer with CPU 1300MHz and above. We are working mainly on AMD Athlon XP 1700+ under Microsoft Windows 2000. Download the installation file from the Download site. Run it. During instalation process you can choose the e.g. destination directory. The aplication will run automaticaly.
Note: There is one bug - when starting the aplication second time via shortcut on the desktop, the error alert will appear. Solution: run manualy the file image-analysis.exe, which is located in directory you specified during installation(default is Program Files\Naja-ia) or right-click on the shortcut, choose Properties and into field Start in copy the path to the program(e.g. C:\Program files\Naja-ia\) and click to OK.

Getting images for analysis

For the analysis it is possible to use all common formats of images, but we recommend the uncompressed formats(e.g. TIF or BMP). The images can be acquired by scanner or digital camera (we use digital camera in flow-box in order to keep the culture out of contamination) in resolution 1600 x 1200 pixels. When using a camera, use a white board with a reference square of 50% grey. The square is available in the Download section. You can download and print it. 

Image preparation

After transfering image(s) into computer open the image in some image editing software(e.g. GIMP - it is available for free). Apply the Gaussian blur filter(with diameter 20pixels) on the grey square. Crop the image to inner side of the Petri dish. The reference grey field must be in left lower corner - you need to rotate the image when the field is in another corner.

Image analysis

Run the program. On the right panel choose the directory, where are the images for analysis or choose directly the file you want to analyze. If you have the image(s) with the grey field, you can simply click to Run process button. The program will  create in the chosen directory three subdirectories: Result, Thumb.gray and Thumb.orig. In the Thumb.* directories are saved the thumbnails of analyzed images or their saturation respectively.
If you do not have images with grey field, choose the Settings tab on  the left panel and unmark the field Correct color.
It is also possible to analyze whole images without color correction - this you may choose also in Settings tab.

Results

The file results.csv with results is located in directory Result mentioned above. You can open it with e.g. table processors( Microsoft Excel, OpenOffice Calc etc.). In it's first row the names of analyzed files and in second row number of analyzed pixels in each file are metioned. In next rows are corrected numbers of pixel of each grey channel. Row 260 contains sums of pixels. In order to get comparable results it is necessary to divide sum of pixels (row 260) by number o analyzed pixels (row 2) [in next version will be done during analysis].