Abstract
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 count and Plot HIstograms of Colony Size (countPHICS) consists of two parts: (1) a macro written for ImageJ which analyses computerised images of cell culture dishes or 6-well plates, counts colonies, estimates their size and saves the results in a text file; (2) a program written with QT Creator which reads the text file, plots histograms of colony size distribution and fits the best function. The full program is freely available at: http://www.fuw.edu.pl/~bbrzozow/FizMed/countPHICS.html. In conclusion, our new publically available software will facilitate colony counting and provide additional information on the colony growth rate, which is relevant especially for radiosensitisation studies.
Highlights
The clonogenic cell survival assay (CCSA) is a basic method used in radiation biology and toxicology to estimate the cytotoxic effect of physical or chemical toxins
While the colony number can be quantified by eye, the analysis of colony size requires some kind of measurement
The software tested for colony size distribution analysis is divided into two parts: the macro which allows us to measure the size of the automatically counted colonies and the program dedicated to draw distributions of colony sizes in the form of histograms
Summary
The clonogenic cell survival assay (CCSA) is a basic method used in radiation biology and toxicology to estimate the cytotoxic effect of physical or chemical toxins. It was introduced in 1955 by Puck et al (Puck et al 1956) following the discovery that cells grown under in vitro conditions require conditioned medium if they are to form colonies from a single precursor (Sanford et al 1948). The area of a colony can be estimated by measuring its diameter but this assumes a round shape which is often not
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