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. 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. In CoCoNut (top), numbers indicate the number of colonies contained within each scoring region, while they have just an ordering function in CAI, where regions can contain only 1 colonyĬlonogenic assays are powerful tools for testing cell reproductive death after biological damage caused by, for example, ionizing radiation. This example (180501 HeLa Flask/7.jpg) illustrates how false positives by CAI (bottom) can counterbalance underestimated colony counts. The same region was used in B and D, while AutoCellSeg does not provide such feature but it always analyzes the whole picture.įig C. The yellow circle in A shows the region of interest selected in CoCoNut for the analysis. Red circles were added in post-production in correspondence to the counted cell clones in order to simplify the comparison. 171214 V79 Dish/1.jpg is used as an example to show how scoring decisions change among different tools. We have tested uniform lighting using the X-Rite ColorChecker White Balance target (on the top) as described in the article.įig B. In the figure, we compare our own office flatbed scanner (A, on the left, WorkCentre 7775, Xerox, Ballerup, Denmark) with the CoCoNut light-box (B, on the right), which was coupled to the Canon camera described in the paper. S1 Fig: The supporting information file contains three figures, labeled A, B, and C.įig A.
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