Camilo Guzmán^1,2, Manish Bagga^1,2, Amanpreet Kaur¹, Jukka Westermarck¹, and Daniel Abankwa¹

¹Turku Centre for Biotechnology, University of Turku, Åbo Akademi University
²Equal contribution

Clonogenic assays measure the survival and growth of a single mammalian cell into a colony. These colony or focus formation assays are widely used in radiation biology and cancer biology, where they are employed to study resistance of cancer cells to radiation or the transforming potential of genes, respectively.

We have developed ColonyArea, an ImageJ-plugin that is optimized to perform standard analysis of colony formation assays conducted in 6- to 24-well dishes. The plugin processes each well individually and determines not the colony number, but the area of the well covered with cells, also taking the intensity into account.

ColonyArea can be installed either through Fiji Update Sites or manually.

In the Fiji menu, go to Help -> Update... -> Manage update sites and select the ColonyArea site. Click Close then Apply Changes. Restart Fiji. In the Plugins dropdown of the Fiji menu, ColonyArea should now be available.

Download the latest release from the repository. Copy the following files to your Fiji plugins directory:

• Colony_area.class
• Colony_measurer.ijm
• Colony_thresolder.ijm
• Manual_colony_thresholder.ijm

Restart Fiji. In the Plugins dropdown of the Fiji menu, ColonyArea should now be available.

Detailed usage instructions and examples here.

Sample image files used in the manual can be downloaded here.

If you use this tool, please cite this paper:

Guzmán C, Bagga M, Kaur A, Westermarck J, Abankwa D.
ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
PLoS One. 2014 Mar 19;9(3):e92444. doi: 10.1371/journal.pone.0092444. PMID: 24647355; PMCID: PMC3960247.

@article{Guzman_ColonyArea_An_ImageJ_2014,
author = {Guzmán, Camilo and Bagga, Manish and Kaur, Amanpreet and Westermarck, Jukka and Abankwa, Daniel},
doi = {10.1371/journal.pone.0092444},
journal = {PloS ONE},
month = {3},
number = {3},
title = {{ColonyArea: An ImageJ plugin to automatically quantify colony formation in clonogenic assays}},
volume = {9},
year = {2014}
}

Beginning in October 2022, maintenance of this plugin is handled by Turku BioImaging, a broad-based, interdisciplinary science and infrastructure umbrella that aims to unite bioimaging expertise in Turku and elsewhere in Finland. Turku BioImaging is jointly operated by the University of Turku and Åbo Akademi University.

For more information and support, email [email protected]