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Freeware tool for analysing numbers and sizes of cell colonies
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Warsaw, Poland.ORCID iD: 0000-0003-0247-697X
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Number of Authors: 62019 (English)In: Radiation and Environmental Biophysics, ISSN 0301-634X, E-ISSN 1432-2099, Vol. 58, no 1, p. 109-117Article in journal (Refereed) Published
Abstract [en]

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/similar to 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.

Place, publisher, year, edition, pages
2019. Vol. 58, no 1, p. 109-117
Keywords [en]
Clonogenic cell survival assay, Colony counter, Colony size histogram, countPHICS
National Category
Biological Sciences Radiology, Nuclear Medicine and Medical Imaging
Identifiers
URN: urn:nbn:se:su:diva-167642DOI: 10.1007/s00411-018-00772-zISI: 000459547400011PubMedID: 30673853OAI: oai:DiVA.org:su-167642DiVA, id: diva2:1303051
Available from: 2019-04-08 Created: 2019-04-08 Last updated: 2019-04-08Bibliographically approved

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Brzozowska, BeataLundholm, Lovisa
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Department of Molecular Biosciences, The Wenner-Gren Institute
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