Colony counter imagej for mac9/4/2023 The CoCoNut software and the 3D-printer files are provided as supporting information (S1 CoCoNut Files). Among its advantages, we highlight the possibility of combining the macro with a perfectly reproducible 3D-printed light-box. The method is inexpensive and easy to obtain. 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. CoCoNut software calibration is fast it requires the adjustment of a single parameter that is the smallest colony area to be counted. CoCoNut proved able to successfully distinguish between single and merged colonies and to identify colonies bordering on flask edges. This counter seems to work best with 8 bit images so if image is 16 bit (images from the Alphaimager are 16 bit), change to 8 bit with image>type>8-bit. ![]() Results were compared to other freely available tools. Restart imageJ and choose plugins>colony counter 4. The full method was tested with V79 and HeLa cell survival samples. In this way, CoCoNut avoids using aggressive background removal filters that usually lead to suboptimal colony count recovery. 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. any unwanted element in the picture) in a minimally invasive manner. Careful attention was given to the image acquisition process, which allows background removal (i.e. It consists in an ImageJ macro and a photographic 3D-printed light-box, conceived and demonstrated to work together for Crystal Violet-stained colonies. 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). Traditionally, the methods require a cumbersome, slow and eye-straining manual counting of viable colonies under a microscope. ![]() Clonogenic assays are powerful tools for testing cell reproductive death after biological damage caused by, for example, ionizing radiation.
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