Fig. 3

Parameters for detection optimization. a A screenshot of the user interface of the ACDC software. b The interface that appears when the “Tune Parameters” option in the left panel in part (A) is selected. The user can manipulate four parameters that aid in detection optimization of candidate cilia (blue dashed box). Signal-to-noise ratio (SNR) compares the intensity of a cilium to the intensity of surrounding background. SNR values range from 1.0 to 2.0. Minimum cilia length values range from 0 to 100 pixels. Users can assign a distance per pixel. Brightness standard deviation accounts for the distribution of different pixel intensities along the entire cilium. Standard deviation values range from 0 to 0.50. Directional score accounts for cilia curvature. Cilia with high directional scores are straighter and rod-like, while cilia with low directional scores are curvier and spherical. Directional threshold values range from 0.01 to 0.51. Higher parameter threshold values result in the rejection of more candidates. c Examples of primary cilia with different values for SNR, cilia length, directional threshold, and standard deviation. Typically, candidates with higher parameter values, aside from length, are more likely to be true cilia, but it is still possible for non-cilia objects such as bright aggregates to be selected