e. Mann–Whitney U) or the Wilcoxon signed rank test (for paired samples) was used. The similarity PR171 between cell distributions in different habitats was assessed by calculating for each habitat the average difference to habitats inoculated from the same set of initial cultures ( same >) and the

average difference to habitats inoculated from different sets of initial cultures ( different >). For devices of types-1 and 2 these differences were calculated using habitats on all devices of a given type, while for devices of type-5 comparisons were only made between habitats located on the same device. To test selleck compound whether there is a significant difference between OSI-906 research buy same > and different > for the devices of types 1 and 2 we used a randomization test. To get a single observable per habitat, the ratio of these

two differences was taken: d relative  = < d same  >/< d different  >, when d relative is smaller than 1 patterns are less different when they are inoculated from the same set of cultures. The difference between spatiotemporal patterns is a comparative measure; the ratio d relative of a given habitat therefore depends on the patterns in all other habitats. To deal with this dependence between data points we assessed significance using a randomization test, where we randomize with respect to the set of initial cultures. For each device type (type 1 and 2) we calculated Fludarabine cost the average of the log transformed d relative () by averaging over all habitats, we then recalculated this measure after randomizing the spatiotemporal patterns by assigning each observed spatiotemporal pattern to a randomly chosen habitat. The randomizations were performed 10.000 times and p-values were calculated by taking the fraction of cases where after randomization was smaller than the

of the original, non-randomized, data set. Two devices of type 2 were both inoculated from the same set of initial cultures (Devices 10 and 11, Additional files 3 and 11), for this analysis the habitats on these devices were grouped together. Strain neutrality Neutrality of the strains during bulk growth has been previously described [42] and was confirmed here by measuring the average doubling time of cultures during the 3.5 hours of growth before inoculation of the devices. There was no significant difference in the average doubling time of strains JEK1036 (green) and JEK1037 (red, mean ± sd = 35.5 ± 2.0 min and 36.0 ± 2.6 min respectively, paired Student’s t-test, p = 0.06, N = 23). Growth curves for the two strains in bulk conditions are shown in Additional file 1. To test for marker neutrality during growth in the microfabricated devices, we compared the occupancies of the two strains in the habitats.