Yeast Colony Counter.


Yeast colony counter is a tool for batch processing of images of Petri dishes with yeast colonies. It evaluates two parameters: the relative coverage of the dish, and the number of colonies in the dish. The tool is designed for use in a research laboratory, where manual manipulation of the dishes and a general-purpose imaging system are utilised, rather than in a specialized commercial laboratory. Processing of dishes with dark background is assumed.

The tool performs automatic thresholding of the image, dish localization and image segmentation. The images are checked for corectness (conditions as "dish partly out of image" or "dish image too small" are evaluated). Currently, it accepts .jpg and .tiff images, other formats may be added on request. The results are stored in a CSV-file - see documentation for more details.

The tool provides simple graphical editor for correction of the machine counting result.

The tool is citeware. If you find it useful for your purpose, we will be thankful if you cite our paper Schier, J., Kovář, B.: Automated counting of yeast colonies using the Fast Radial Transform algorithm, BIOSTEC 2011 4th International Joint Conference on Biomedical Engineering Systems and Technologie, Rome, Italy, 2011, see also

Note! The tool has been moved

The author of the tool, Dr. Jan Schier, is no longer with the Department of Signal Processing. For this reason, you can find the current version of the package at the following address. The package located here will no longer be maintained.

Package Summary

Title Yeast Colony Counter
License BSD-like license
(See the 'license.txt' file in the package.)
Package content ZIP archive with application (Windows executable), documentation, and four example dish images
Size 272674656 Bytes (260 MB)
MD5 checksum 4218efce9247fdbc34caa587de0c349d
Required tools
& platform
MS Windows
Installation notes
  • Download package
  • Unzip package
  • Run the 'tool\ColonyCounter_pkg.exe' self-extracting archive for tool installation
    See the 'readme.txt' and 'doc\ColonyCounter.pdf' files in the package.

Result Category

Project number Contract section Year RIV category Comment
1M0567 VS1 4 S authorized SW

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Contact Person

Please, don't hesitate to contact Zdenek Pohl to obtain more information.