Yeast Colony Counter

YeastColonyCounter screenshot

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


The development of the tool has been supported from the research project 1M0567 of the Ministry of Education, Youth and Sports and later from the project TA01010931 of the Technology Agency of the Czech Republic.

The tool is free for educational and/or research purpose and can be downloaded after filling this form.

Documentation in pdf file1.35 MB