Extensive research using penetrating electrodes implanted in the central and peripheral nervous systems has been performed for many decades with significant advances made in recent years. While penetrating devices provide proximity to individual neurons in vivo, they suffer from declining performance over the course of months and often fail within a year. 2D histology studies using serial tissue sections have been extremely insightful in identifying and quantifying factors such as astroglial scar formation and neuronal death around the implant sites that may be contributing to failures. However, 2D histology has limitations in providing a holistic picture of the problems occurring at the electrode-tissue interface and struggles to analyze tissue below the electrode tips where the electrode tracks are no longer visible. In this study, we present 3D reconstruction of serial sections to overcome the limitations of 2D histological analysis. We used a cohort of software: XuvStitch, AutoAligner, and Imaris coupled with custom MATLAB programming to correct warping effects. Once the 3D image volume was reconstructed, we were able to use Imaris to quantify neuronal densities around the electrode tips of a hybrid microelectrode array incorporating Blackrock, Microprobes, and NeuroNexus electrodes in the same implant. This paper presents proof-of-concept and detailed methodological description of a technique which can be used to quantify neuronal densities in future studies of implanted electrodes.
Keywords: 3D reconstruction; confocal microscopy; dewarping; foreign body response; histology; image registration; intracortical microelectrode; serial section.