Computational protocol: Three-dimensional analysis of synapses in the transentorhinal cortex of Alzheimer’s disease patients

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Protocol publication

[…] To analyze the spatial distribution of synapses, Spatial Point Pattern analysis was performed as described elsewhere [, ]. Briefly, we compared the actual position of centroids of synapses with the Complete Spatial Randomness (CSR) model — a random spatial distribution model which defines a situation where a point is equally likely to occur at any location within a given volume. For each of the 30 different samples, we calculated three functions commonly used for spatial point pattern analysis: G, F and K functions (for a detailed description, see []). An additional step to explore the spatial distribution of a spatial pattern is to obtain the distance to the nearest neighbor. To do this, the distance of each synapse to its nearest synapse was measured, and comparison between control and AD patients was also performed. This study was carried out using the Spatstat package and R Project program []. [...] To determine possible differences between groups, statistical comparisons of synaptic density, proportion of synapses, TEC thickness, synaptic size (SAS), neuronal and glial cell bodies, blood vessels and neuropil volume fraction, as well as the distance to the nearest neighbor were carried out using the unpaired Mann-Whitney (MW) nonparametric U-test (the normality and homoscedasticity criteria were not met). Frequency distribution analysis of the SAS was performed using Kolmogorov-Smirnov (KS) nonparametric test. Statistical studies were performed with the aid of the GraphPad Prism statistical package (Prism 5.00 for Windows, GraphPad Software Inc., USA) and SPSS program (IBM SPSS Statistics v22, IBM Corp., USA). […]

Pipeline specifications

Software tools spatstat, SPSS
Applications Miscellaneous, Conventional fluorescence microscopy
Organisms Homo sapiens
Diseases Adrenal Cortex Diseases, Alzheimer Disease, Liver Diseases