A Semi-Automatic Software Tool for Batch Processing of Yeast Colony Images

Jan Schier and Bohumil Kovář

Keywords

yeast colonies, Petri dish, image segmentation, fast radial transform

Abstract

A software application for batch counting of yeast colonies in images of Petri dishes, based on the fast radial transform by Loy and Zelinsky, is introduced in the paper. The motivation to develop our own tool, instead of using a commercial solution, was mainly the requirement to reuse the imaging equipment already existing in the cooperating genetics laboratory, as well as the possibility to adapt the application to the needs of the laboratory. The basic aim is to process image sets prepared beforehand in the darkroom and to automate the process of counting as much as possible. The tool operates either in a fully automatic mode, or provides an interactive editor for correction of the initial machine counting result. The underlying processing flow and algorithms are reviewed in the paper and the performance of the method is evaluated, using a test set of 245 images. The application is available for download or can be requested from the authors of the paper, in both cases free of charge.

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