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. Author manuscript; available in PMC: 2022 Feb 15.
Published in final edited form as: J Neurosci Methods. 2020 Dec 15;350:109038. doi: 10.1016/j.jneumeth.2020.109038

Table 1.

Comparison of the total number of Rab5-immunoreactive early endosomes quantified in each ChAT-immunoreactive BFCN in ImageJ and Imaris. A Wilcoxon-Mann-Whitney test showed statistically a significant difference in the number of early endosomes identified by each program (z = 2.3434, p = 0.028), with approximately twice the number of early endosomes counted per BFCN in ImageJ compared to Imaris.

BFCN number Number of z-slices in original stack Total Number of Rab5-immunoreactive early endosomes per neuron
ImageJ Imaris
1 33 182 97
2 33 162 80
3 27 118 65
4 36 142 58
5 29 128 62
6 33 157 56
Mean (± St Dev): 148.17 (± 23.53) 69.67 (±15.85) p=0.0281