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OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

Figure 5

Comparison of robustness to common perturbations between OpenCFU, NICE [13] and an ImageJ macro [10].

A qualitative assessment of robustness was undertaken by analysing pictures containing artefacts (A). Representative portions of 1.7 cm by 1.7 cm (200200 pixels) illustrate the results of the presence of bubbles (1), cracks in the agar (2), dust (3) and edge of dish (4) in the region of interest. Objects detected by OpenCFU, NICE and the ImageJ macro (IJM) are represented by ellipses, crosses and arbitrary colours, respectively. NICE and IJM but not OpenCFU seemed to consistently detect artefacts as colonies. A quantitative analysis of robustness to plate mispositioning was conducted (B). OpenCFU, NICE and IJM were used to count the number of colonies in the pictures of 19 plates. Then, all the images were translated by 1.7 mm (25px) and analysed with the same region of interest as the original. This procedure induced a significant bias for NICE, (-) colonies and IJM (-) colonies, but not for OpenCFU (-) colonies (one-sided paired t-test). The impact of the presence of bubbles in the agar was measured by analysing pictures of 18 plates containing exclusively bubbles (C). A linear regression between the number of bubbles and the number of detected objects was performed. NICE and IJM counts were both positively related to the number of bubbles, (-) and (-), respectively. OpenCFU was not affected: (-.

Figure 5