AUTOMATED COUNTING OF YEAST COLONIES USING THE FAST RADIAL TRANSFORM ALGORITHM

Jan Schier, Bohumil Kovář

Abstract

A method for counting yeast colonies in images of Petri dishes, based on the fast radial transform by Loy and Zelinsky, is introduced and evaluated in the paper. The characteristic properties of the images of yeast colonies, as produced by the setup used in the cooperating genetics laboratory, are described, the underlying counting algorithm is reviewed and the performance of the method is evaluated, using a test set of 245 images. The images, included in this set, typically contained between 10 and 70 colonies per dish, with relative coverage of the diosh less than 10% of the area. The average counting error (missed colonies) on this set was under 4%. A tool, implementing the method, has been developed in Matlab. The motivation to develop our own colony counting program, instead of using a commercial solution, was to reuse the imaging equipment already existing in the laboratory and to adapt the tool to the needs of this laboratory. The tool provides a batch mode for processing of larger image sets prepared beforehand in the darkroom and it automatizes the process of counting as much as possible. It is available for download or can requested from the authors of the paper, in both cases free on charge.

References

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Paper Citation


in Harvard Style

Schier J. and Kovář B. (2011). AUTOMATED COUNTING OF YEAST COLONIES USING THE FAST RADIAL TRANSFORM ALGORITHM . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 22-27. DOI: 10.5220/0003129000220027


in Bibtex Style

@conference{bioinformatics11,
author={Jan Schier and Bohumil Kovář},
title={AUTOMATED COUNTING OF YEAST COLONIES USING THE FAST RADIAL TRANSFORM ALGORITHM},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={22-27},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003129000220027},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - AUTOMATED COUNTING OF YEAST COLONIES USING THE FAST RADIAL TRANSFORM ALGORITHM
SN - 978-989-8425-36-2
AU - Schier J.
AU - Kovář B.
PY - 2011
SP - 22
EP - 27
DO - 10.5220/0003129000220027