Cell colony counter called CoCoNut

Mattia Siragusa*, Stefano Dall'Olio, Pil M. Fredericia, Mikael Jensen, Torsten Groesser, Hamidreza Montazeri Aliabadi (Editor)

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Clonogenic assays are powerful tools for testing cell reproductive death after biological damage caused by, for example, ionizing radiation. Traditionally, the methods require a cumbersome, slow and eye-straining manual counting of viable colonies under a microscope. To speed up the counting process and minimize those issues related to the subjective decisions of the scoring personnel, we developed a semi-automated, image-based cell colony counting setup, named CoCoNut (Colony Counter developed by the Nutech department at the Technical University of Denmark). It consists in an ImageJ macro and a photographic 3D-printed light-box, conceived and demonstrated to work together for Crystal Violet-stained colonies. Careful attention was given to the image acquisition process, which allows background removal (i.e. any unwanted element in the picture) in a minimally invasive manner. This is mainly achieved by optimal lighting conditions in the light-box and dividing the image of a flask that contains viable colonies by the picture of an empty flask. In this way, CoCoNut avoids using aggressive background removal filters that usually lead to suboptimal colony count recovery. The full method was tested with V79 and HeLa cell survival samples. Results were compared to other freely available tools. CoCoNut proved able to successfully distinguish between single and merged colonies and to identify colonies bordering on flask edges. CoCoNut software calibration is fast; it requires the adjustment of a single parameter that is the smallest colony area to be counted. The employment of a single parameter reduces the risk of subjectivity, providing a robust and user-friendly tool, whose results can be easily compared over time and among different bio-laboratories. The method is inexpensive and easy to obtain. Among its advantages, we highlight the possibility of combining the macro with a perfectly reproducible 3D-printed light-box. The CoCoNut software and the 3D-printer files are provided as supporting information (S1 CoCoNut Files).
Original languageEnglish
Article numbere0205823
JournalPLOS ONE
Volume13
Issue number11
Number of pages18
ISSN1932-6203
DOIs
Publication statusPublished - 2018

Cite this

Siragusa, M., Dall'Olio, S., Fredericia, P. M., Jensen, M., Groesser, T., & Montazeri Aliabadi, H. (Ed.) (2018). Cell colony counter called CoCoNut. PLOS ONE, 13(11), [e0205823]. https://doi.org/10.1371/journal.pone.0205823
Siragusa, Mattia ; Dall'Olio, Stefano ; Fredericia, Pil M. ; Jensen, Mikael ; Groesser, Torsten ; Montazeri Aliabadi, Hamidreza (Editor). / Cell colony counter called CoCoNut. In: PLOS ONE. 2018 ; Vol. 13, No. 11.
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abstract = "Clonogenic assays are powerful tools for testing cell reproductive death after biological damage caused by, for example, ionizing radiation. Traditionally, the methods require a cumbersome, slow and eye-straining manual counting of viable colonies under a microscope. To speed up the counting process and minimize those issues related to the subjective decisions of the scoring personnel, we developed a semi-automated, image-based cell colony counting setup, named CoCoNut (Colony Counter developed by the Nutech department at the Technical University of Denmark). It consists in an ImageJ macro and a photographic 3D-printed light-box, conceived and demonstrated to work together for Crystal Violet-stained colonies. Careful attention was given to the image acquisition process, which allows background removal (i.e. any unwanted element in the picture) in a minimally invasive manner. This is mainly achieved by optimal lighting conditions in the light-box and dividing the image of a flask that contains viable colonies by the picture of an empty flask. In this way, CoCoNut avoids using aggressive background removal filters that usually lead to suboptimal colony count recovery. The full method was tested with V79 and HeLa cell survival samples. Results were compared to other freely available tools. CoCoNut proved able to successfully distinguish between single and merged colonies and to identify colonies bordering on flask edges. CoCoNut software calibration is fast; it requires the adjustment of a single parameter that is the smallest colony area to be counted. The employment of a single parameter reduces the risk of subjectivity, providing a robust and user-friendly tool, whose results can be easily compared over time and among different bio-laboratories. The method is inexpensive and easy to obtain. Among its advantages, we highlight the possibility of combining the macro with a perfectly reproducible 3D-printed light-box. The CoCoNut software and the 3D-printer files are provided as supporting information (S1 CoCoNut Files).",
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Siragusa, M, Dall'Olio, S, Fredericia, PM, Jensen, M, Groesser, T & Montazeri Aliabadi, H (ed.) 2018, 'Cell colony counter called CoCoNut', PLOS ONE, vol. 13, no. 11, e0205823. https://doi.org/10.1371/journal.pone.0205823

Cell colony counter called CoCoNut. / Siragusa, Mattia; Dall'Olio, Stefano; Fredericia, Pil M.; Jensen, Mikael; Groesser, Torsten; Montazeri Aliabadi, Hamidreza (Editor).

In: PLOS ONE, Vol. 13, No. 11, e0205823, 2018.

Research output: Contribution to journalJournal articleResearchpeer-review

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AU - Siragusa, Mattia

AU - Dall'Olio, Stefano

AU - Fredericia, Pil M.

AU - Jensen, Mikael

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A2 - Montazeri Aliabadi, Hamidreza

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AB - Clonogenic assays are powerful tools for testing cell reproductive death after biological damage caused by, for example, ionizing radiation. Traditionally, the methods require a cumbersome, slow and eye-straining manual counting of viable colonies under a microscope. To speed up the counting process and minimize those issues related to the subjective decisions of the scoring personnel, we developed a semi-automated, image-based cell colony counting setup, named CoCoNut (Colony Counter developed by the Nutech department at the Technical University of Denmark). It consists in an ImageJ macro and a photographic 3D-printed light-box, conceived and demonstrated to work together for Crystal Violet-stained colonies. Careful attention was given to the image acquisition process, which allows background removal (i.e. any unwanted element in the picture) in a minimally invasive manner. This is mainly achieved by optimal lighting conditions in the light-box and dividing the image of a flask that contains viable colonies by the picture of an empty flask. In this way, CoCoNut avoids using aggressive background removal filters that usually lead to suboptimal colony count recovery. The full method was tested with V79 and HeLa cell survival samples. Results were compared to other freely available tools. CoCoNut proved able to successfully distinguish between single and merged colonies and to identify colonies bordering on flask edges. CoCoNut software calibration is fast; it requires the adjustment of a single parameter that is the smallest colony area to be counted. The employment of a single parameter reduces the risk of subjectivity, providing a robust and user-friendly tool, whose results can be easily compared over time and among different bio-laboratories. The method is inexpensive and easy to obtain. Among its advantages, we highlight the possibility of combining the macro with a perfectly reproducible 3D-printed light-box. The CoCoNut software and the 3D-printer files are provided as supporting information (S1 CoCoNut Files).

U2 - 10.1371/journal.pone.0205823

DO - 10.1371/journal.pone.0205823

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Siragusa M, Dall'Olio S, Fredericia PM, Jensen M, Groesser T, Montazeri Aliabadi H, (ed.). Cell colony counter called CoCoNut. PLOS ONE. 2018;13(11). e0205823. https://doi.org/10.1371/journal.pone.0205823