Counting of yeast colonies in Petri dish images


The package contains demo of counting the yeast colonies in images of Petri dishes. The algorithms, contained in this demo, represent part of a software tool used to determine relative coverage of the dish, to estimate the number of colonies, and, using simple graphical tool, to correct this estimate. The algorithms, contained in the package, perform the necessary preprocessing of an image and estimate the count of colonies. Included are several filters to reduce the estimation noise, separation of round, isolated colonies from the conglomerate blobs and estimation of number of colonies in these conglomerates. The output of the demo are two images: the original (grayscale) image with markings of the dish center and the region-of-interest and the image of the region-of-interest, with crossmarks for the counted colonies and with the figures of relative area and the estimated number of colonies.

Package Summary

Title Counting of yeast colonies in Petri dish images
License GPL
(See the 'gpl.txt' file in the package.)
Package content ZIP archive containing demo running in the Matlab environment, sample images, documentation
Size 9535905 Bytes
MD5 checksum 9b303ab109ef7965051b0ddc4843d2d4
Required tools
& platform
Matlab 2008b, Image Processing Toolbox
Installation notes
  • Download package
  • Unzip package
  • Open the Demo directory in the Matlab environment
  • Run demo by calling the demo.m function
See the 'doc/sw_petri_counting.pdf' file, contained in the package.

Result Category

Project number Contract section Year RIV category Comment
1M0567 VS1 2 S Functional sample (demo)

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Contact Person

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