Automated stereological counting method. (a) A counted area showing the cones. The number of cones after exclusion and before exclusion (in brackets) is mentioned below the image. Cones in contact with the two coordinates (white lines) are automatically excluded. The colored dots represent the increment of the counting process. The colored circle point to excluded objects following the counting parameters (Spotcutoff, Spotsize and SurfSpot, Additional file 4) and counting window. More specifically, from the top to the bottom, the circles mean: Yellow, not satisfying the counting parameters; Black, cross the Y exclusion axe; Red, not satisfying the parameters and Purple, not satisfying the counting parameters. (b) Average cone densities of rd1 and wt retinas using automated stereological counting (n = 7). Error bars show +/- SEM, * p < 0.05, ** p < 0.01, *** p < 0.001.