The automated method using AxonJ avoids experimenter bias in axon identification and does not rely on determination of nerve area since all axons within the nerve are counted. However, plotting AxonJ counts versus manual counts, we found that with our optic nerves, AxonJ tended to undercount axons compared to the manual method, with undercounting increasing with increasing axon number (
Fig. 4A). Because we know from manual counting that delineating axon boundaries at higher densities becomes more challenging, we hypothesized that undercounting by AxonJ is related to axon density. To investigate this possibility, we plotted the ratio of AxonJ counts to manual counts versus axon density, calculated as the total number of axons determined manually divided by the nerve area. As shown in
Fig. 4B, AxonJ undercounting was strongly correlated with axon density (r
2 = 0.71,
n = 60,
P < 0.0001), supporting axon density as a determining factor in the observed undercounting by AxonJ. Using the equation of the best fit line of the AxonJ/manual count ratio versus axon density plot (
Fig. 4B, orange dotted line) and manually determined axon density, a correction factor was applied to AxonJ counts to account for density-dependent undercounting. Plotting corrected AxonJ versus manual counts resulted in a best-fit line that overlaps with the equivalence line (
Fig. 4C), indicating that corrected AxonJ counts are consistent with the gold standard method of manual counting. Similar to results from manual counting, analysis of corrected AxonJ counts (
Fig. 4D) showed statistically significant axon loss for vehicle-treated mice (
P = 0.0027, paired
t-test), with 12 of 13 mice having reduced numbers of axons in nerves from microbead-injected compared to contralateral control eyes. In telmisartan-treated mice, only 10 of 17 showed axon loss, with no significant difference between microbead-injected and control eyes (
P = 0.26, paired
t-test). As shown in
Figure 4E, axon loss in nerves from microbead-injected eyes was significantly greater in vehicle-treated as compared to telmisartan-treated mice (mean [95% CI]: vehicle: 14.2 [6.7 to 21.8]; telmisartan: 2.9 [−4.9 to 10.7] % axon loss,
P = 0.0375, Student's
t-test). These results with automated counting are consistent with those from manual counting and together suggest that telmisartan treatment protected against RGC axon degeneration in response to elevated IOP.