The clonogenic cell survival assay is a basic method to study the cytotoxic effect of radiation and chemical toxins. In large experimental setups, counting of colonies by eye is tiresome and prone to bias. Moreover, it is often interesting to quantify the size of individual colonies. Such analyses are largely facilitated by computerised image analysis systems. Although a number of such systems exist, they all focus on enumerating colonies and not on analysing the colony size. We have developed a new software package for both counting colonies and plotting their size distributions. The software called countPHICS consists of two parts: 1) a macro written for ImageJ which analyses computerised images of petri dishes, counts colonies, estimates their size and saves the results in a text file; 2) the Plotting HIstograms of Colony Size (PHICS) program written with QT Creator which reads the text file, plots histograms of colony size distribution and fits the best function. The program will be freely available at: www.crpr-su.se/colony.