Computational protocol: In Vivo Two-Photon Imaging of Dendritic Spines in Marmoset Neocortex1,2,3

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Protocol publication

[…] We used ImageJ (National Institutes of Health), Neurolucida (MBF Bioscience), and custom-made software written on MATLAB (R2009a; MathWorks) for our image analysis. Images were processed with a median filter (2.0 pixel radius) to reduce noise. Dendrites and spines were traced and marked manually in a three-dimensional space. The loss or gain rate of dendritic spines was calculated as the percentage of spines that appeared or disappeared on day 1, relative to the total number of spines on day 0. The length of spines was measured from the tip of the spine to the interface with the dendritic stalk (). [...] All statistical analyses were performed using R (). We used the Wilcoxon rank sum test to compare between groups, and we corrected for multiple comparisons when required. Differences were considered to be significant at p < 0.05. Measurements are reported as the mean and SD. The values of statistical power were calculated using G*Power ( and are presented in . Experimental animals were randomly assigned to in vivo or ex vivo conditions. […]

Pipeline specifications

Software tools ImageJ, Neurolucida, G*Power
Applications Miscellaneous, Microscopic phenotype analysis
Chemicals Tetracycline