Automated counting of mammalian cell colonies by means of a flat bed scanner and image processing

Background Clonogenic assays are used frequently to measure the cell killing and mutagenic effects of radiation and other agents. Clonogenic assays carried out manually are tedious and time-consuming and involve a significant element of subjectivity. However, several commercial automatic colony counters are available. Based on CCD video imaging and image analysis they are relatively expensive and can analyze only one petri dish at a time. Method We have developed a cheaper and more efficient device, which employs a flat bed scanner to image 12 60-mm petri dishes at a time. Two major problems in automated colony counting are the clustering of colonies and edge effects. By using standard image analysis and implementing an inflection point algorithm, these problems were greatly diminished. The resulting system was compared with two manual colony counts, as well as with automated counts with the Oxford Optronix ColCount colony counter for cell lines V79 and HaCaT. Results Comparisons assuming the manual counts to be correct showed that our automatic counter was slightly more accurate than the commercial unit. Conclusions As a whole, our automated colony counter performed significantly better than the commercial unit with regard to processing time, cost and accuracy. © 2004 Wiley-Liss, Inc.