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Heimo Wolinski, PhD
University Graz
Senior Scientist
Humboldtstrasse 50/II
8010 Graz, Austria
Phone: +43 316 380 5489
Fax: +43 316 380 9854 -------------------------------
Web: IMB-Graz MCF
Web: H. Wolinski Research

Free ImageJ plug-in: flexible SGA colony detector

With this ImageJ plugin you can count, measure the size and calculate the intensity of imaged yeast patches on a solid media plate.

You can download the plugin here. To install it, extract the files and copy them to PATH_TO_IMAGEJ/imagej/plugins/analyze.
Please restart ImageJ.
The name of the plugin should now appear in the ImageJ menue: Plugins->Analyze->Patch Detector Plus.

Open a RGB- or gray value image in ImageJ.

Enter the required data to define the grid (number of patches etc.) in the BDP-plugin. By pressing "return" or clicking on "DrawGrid" a grid will be drawn.

If you set the threshold value to 0 ImageJ will use an automatic calculated threshold value. If you want to use your own threshold value you can enter it there.

Depending on the threshold the colonies will be black (= pixel value 0) or white (= pixel value 255). With the checkbox you can count either 0 or 255.

To modify the rows and columns select "Selection of Rows and Columns" and click on "DrawGrid". You will get a similar image as shown below:

If you click on the numbers you can adjust the corresponding rows and columns.

If you select "Selection of Single Dots" and click on "DrawGrid" you will get a grid like this:

Using this mode you can adjust each individual field. Again click on the the numbers and modify the fields.

Finally click on "Calculate", which will compute size and intensity of the patches or on "CountOnly" for counting the patches only.

As a results you will get the following table:

The table can be exported as an Excel file.

For questions and suggestions do not hesitate to contact me:

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